Took cams off, and think i rotated them when i re installed them, will that mess up my timing?

First, DO NOT start the engine if the mechanical timing is wrong! My next obvious suggestion is to get it to a good mechanic and get them to sort it out for you.
I'm assuming your refering to the Mechanical Timing? Mazda use an 'Interference' engine so read this all the way through BEFORE doing any work. An interference engine means the valves will hit the piston face if the mechanical timing is even slightly out. That is why you don't start your engine with the timing set wrong. It's a VERY expensive repair.
Start from scratch. Remove the chain from the CAMs and cable tie it to something on the top of the engine to stop it disappearing out of sight.
Turn the Crank to about 10 to 15 degrees past Top Dead Centre (TDC). This is to move the pistons away from the valves so you can set the Cam timing marks. Set the Cam marks first then turn the Crank BACK to TDC. As long as the chain marker on the crank sprocket is lined up correctly the Cam chain markers should be correct.
Once you have timed everything into place use a socket and ratchet to turn the Crank pulley bolt Clockwise 2 full rotations. The timing marks should return to the correct positions.

the crank has to be on tdc for the piston position
on the right hand bank ( left side looking at the front of the engine , the top most cam is the inlet cam and the letters RI will be at the 9 oclock position on the top side of the shaft boss on the cam gear the lower cam gear will have the letters re in the same position
on the other bank the top cam gear will have li at the 3 oclock position and the lower cam gear will have re in the same position
use the position as 90 degrees to the head and taken through the cam shaft center

Dual Mass Flywheel, and will also need new clutch Remove the engine coverUsing a [16 mm], rotate the tensioner arm clockwise (about 14° )and remove the belt from the pulley.
Remove the power steering pump pulley, idler pulley, tensioner pulley and crankshaft pulley.
Remove the upper and lower timing belt covers.

Remove the auto tensioner.
NOTE
Rotate the crankshaft clockwise and align the timing mark to set the No.1 cylinder's piston to TDC (compression stroke).
At this time, the timing marks of the camshaft sprocket and cylinder head cover should coincide with each other.




Unbolt the tensioner to remove the timing belt.
NOTE
If you plan to use the timing belt again, mark the rotation direction on the belt so you reinstall it correctly.

SERVICE MANUAL
Applies to: Santa Fe 2004
GROUP
Engine Mechanical System Timing System



INSTALLATION
Install the idler pulley to water pump boss.
NOTE
Insert and install the idler pulley to the roll pin that is pressed in the water pump boss.


Install the tensioner arm and plain washer to the cylinder block.
Install the tensioner pulley to the tensioner arm.
Install the camshaft sprockets and align the timing marks.

NOTE
When installing the camshaft sprockets, fasten them tightly while holding the hexagonal part of the camshaft.
Before installing the timing belt, if the timing marks of the cam sprocket and the cylinder head cover do not coincide, do not rotate the cam sprocket more than 3 teeth in either direction.
Rotating the sprocket more than 3 teeth may allow the valve and piston to touch each other.
If the cam sprocket is rotated more than 3 teeth unavoidably, rotate the crankshaft counter - clock wise a bit before rotating the cam sprocket.
Install the auto tensioner to the front case.
NOTE
At this time auto tensioner's set pin should be compressed and secured with set pin.




Align the timing marks of each sprocket and install the timing belt in the following order. Crankshaft sprocket--> Idler pulley--> camshaft sprocket (LH side)--> Water pump pulley--> camshaft sprocket (RH side)--> Tensioner pulley.
NOTE
In this step, No. 1 cylinder is in the TDC (Compression stroke).
Be very careful if you use your fingers.



Pull out the set pin of the auto tensioner.



Install the upper and lower timing belt covers.
Install the power steering pump pulley, idler pulley, tensioner pulley and crankshaft pulley.
Using the wrench [16mm], rotate the tensioner arm clockwise (about 14°) and install the belt to the pulley.
Install the engine cover.
How to adjust the tension of the timing belt
Rotate the crankshaft 2 turns clockwise and measure the projected length of the auto tensioner at TDC (# 1 Compression stroke) after 5 minutes.
The projected length should be 6-8 mm.
Verify that the timing marks of each sprocket are in their specified position.
NOTE
If the timing marks are not in their specified position, repeat from 6 above.

During most engine rebuilds, a completely new timing assembly should be installed. If wear exists on any component, replacement of the entire assembly is necessary. Wear in the chain, gears, or sprockets means a timing lag, which results in poor engine performance.
The timing chain or belt is generally installed with the gears in their correct positions. Before installing a new chain, soak it in oil.
OHC (Overhead Cam) Engines
Some OHC engines use a chain drive; others use a belt drive. Removing the cover on some OHC engines that have timing chains is more difficult, because the cover often fits between the oil pan and the cylinder head. There are special procedures for replacing cam timing components in these engines.
Before a chain repair job, perform a leakage test on non-freewheeling engines to check for bent valves, so that an accurate repair estimate can be made.
OHV (Overhead Valve) Pushrod Engines
On many OHV pushrod engines, the crankshaft sprocket is installed on the crankshaft nose and the crankshaft is rotated to position piston #1 at TDC. At this point, a mark stamped onto the crankshaft sprocket is pointing directly upward (toward the camshaft).
The camshaft sprocket is then temporarily bolted to the cam and used to rotate the cam until a mark stamped on the cam sprocket is pointing directly downward (toward the crankshaft). The sprocket is then removed from the cam (without allowing the cam to rotate).
The timing chain is looped over the cam gear, the mark on the cam gear is positioned directly downward, and the chain is looped around the crankshaft sprocket. When the cam sprocket is attached to the cam, the timing marks on the crank and cam sprockets should be pointing toward one another. NOTE THIS IS FOR 2WD 4.0

Once the belt is removed, turn the crank pulley clockwise until the pin on the crank nut lines up with the notch at the 12 o'clock position just above it. The intake cam needs to be rotated so the "I" on the pulley is at the 12 o'clock position and the exhaust cam needs to be rotated so the "E" on the pulley is at the 12 o'clock position, then install the belt and adjust tension. Use a 1/2" drive ratchet and I think a 21mm socket for the crank pulley and a 17mm wrench for the cam pulleys.

It is normal for the exhaust cam to be slightly off during a rotation because of the nature of the VCT mechanisim. It uses oil pressure to change the cam angle. Since there is no oil pressure with the engine off, it won't stop in the same place every time. Check the links below for more information:

Timing Part 1

Timing Part 2

You did it the right way. If you tried to make a full cam revolution you would have hit the pistons with the valves. Put the lower timing cover and crank pulley back on. If the cam marks are aligned right and the mark on the lower timing cover lines up with the mark on the crank pulley, you're good to go.

Removal & Installation

1. Disconnect the negative battery cable.
   
2. Rotate the auto tensioner clockwise to release tension, then remove the drive belt.
   

To install:

1. Install drive belt (A). Route the belt over the components in the following order: Crankshaft pulley → A/C pulley → idler pulley → generator pulley → water pump pulley → P/S pump pulley → tensioner pulley.
   
2. Rotate auto tensioner arm in the counter-clockwise moving auto tensioner pulley bolt with wrench.
   
3. After putting belt on auto tensioner pulley, release the auto tensioner pulley slowly.
   Accessory serpentine belt routing—3.5L engine
   Accessory serpentine belt (A) routing—3.8L engine
   

Check the timing marks a be sure that when you turned the camshaft you do not advertently cause a belt problem. You should never rotate the engine or camshaft by the camshaft bolt when the timing belt is engaged, the lower drive pulley is smaller than the cam pulley so it become very easy to put a large torque load on the lower pulley by turning the upper one with the belt on, chances are you may have popped the belt a tooth, and the engine is no longer in time, if timing is not correct inspect the full length of the belt and replce if neccessary. Hope this helps, let me know.

well not sure exactly why it wont line up use something to turn the crank and cam to appropiate position start sliding crank gear until cam gear is touching then start to push both at same time make sure your crank key and cam pin are bothin place On many OHV pushrod engines, the crankshaft sprocket is installed on the crankshaft nose and the crankshaft is rotated to position piston #1 at TDC. At this point, a mark stamped onto the crankshaft sprocket is pointing directly upward (toward the camshaft).
The camshaft sprocket is then temporarily bolted to the cam and used to rotate the cam until a mark stamped on the cam sprocket is pointing directly downward (toward the crankshaft). The sprocket is then removed from the cam (without allowing the cam to rotate).
The timing chain is looped over the cam gear, the mark on the cam gear is positioned directly downward, and the chain is looped around the crankshaft sprocket. When the cam sprocket is attached to the cam, the timing marks on the crank and cam sprockets should be pointing toward one another.