How do I replace pipes in back of engine for heater

Does this 'pipe/tube' come through the bulkhead at the back of the engine bay from inside the car or is it on or near the actual engine? Could you comment below with another 'close up' photo of the the actual pipe?
If it is one of the two pipes poking through the bulkhead, it could be the 'Heater Matrix'. This is one of those jobs that to change the actual part is easy but getting to the part is a total pain in the tail bone. A 'take the Dashboard out' job.
Replacing most pipes, hoses and tubes will depend on what is at each end of it. Most short sections can be replaced if they are not part of something else like a water pump or a thermostat housing.

the easiest way is to remove the pipes to it from engine bay and use a copper pipe to bridge the pipes, so you will need to cut the ends off and use some jubiees on the pipes to secure it to the copper pipe standard house hold size copper pipe, if you do need to cut ends off make sure you leave and inch and a half on them so you can fix them back on when the heater core is replaced or fixed. just to recommend i would fix the core as soon as possible

Sounds like an air lock!
To Check....
With engine cold set heater to hot position.
ID return pipe from heater under the hood. Remove the return pipe at one end to check if coolant is there ( it should run from heater pipe) if no coolant you have an air lock.
To remove air lock top up coolant header when engine is cold. Leave heater in cold position replace pipe and start engine. Allow it to come to working temp then set heater to hottest position. Allow a few seconds and check if the pipe you first removed is hot. If no then ease the securing clip and carefully allow air to escape while engine is running... place a cloth over this area to prevent hot coolant spraying out. When coolant appears re-tighten pipe.
"PLEASE BE VERY CAREFUL DOING THIS AS COOLANT WILL BE EXTREMELY HOT".
If you're not confident enough to do this ask a qualified mechanic to do it for you.
Again please be careful.

On the fire wall of the engine compartment you will find 2 rubber hoses connected to 2 Brass or Aluminum pipes that stick out of the engine firewall, loosen the clamps and remove those hoses, one hose and pipe is smaller than the other hose and pipe, force water with a garden hose through the smaller pipe to "backflush the heater core. Below is a picture of the core and the pipes that come out in the engine compartment to give you an idea what to look for, I have also provided a picture of the heater hoses from the engine.

Check heater pipes under the vehicle, as these have heater controls in the back of the car the pipes rust out causing coolant to leak out. cut the pipes and bridge them together as you dont require a heater in the rear of the vehicle. Costly if you cook the engine if its a V6, as you have to pull the engine out to do head gasket replacement.

There are two heater hoses, each appx. 1 inch wide, that run from the engine and hooks up to the heater core, behind your dashboard. The heater core's two connection pipes stick out from the firewall of your jeep and you have to attach the two heater hoses to those two pipes. If someone disconnected your heater, they probably just joined together the two heater hoses, that run from your engine, so now you'll have to disconnect that joining and reattach the hoses to the heater core pipes. That way, hot coolant will flow into the heater core to warm you up.

It is most probably the problem with blend door or blend door actuator. But just in case I would suggest to follow the entire procedure:

First you have to identify what causes the problem.
To do this you have to:
1) When engine is cold check the level of coolant. If it is low fill it up.
2) Start engine and check if engine reaches regular temperature. If your engine is not heated enough it means your thermostat does not work properly and should be replaced
3) If engine temperature is normal, then check the temperature of pipes that go to/from heater core. These pipes are located up the fire wall (easier access is from the passenger side). If pipe/pipes are cold (even engine is warm) it means you heater core is plugged and should be flushed. Keep in mind, flushing the whole cooling system is different from flushing heater core.
4) If pipe/pipes are hot/warm, turn off the fan, switch controller to the hot position, wait for 3-4 minutes and turn on the fan. Note if the cold air blows first or warm air blows first but it cools down in 5-10 seconds. If the air blows cold than it is most probably the problem with blend door or blend door actuator.
5) If air blows warm first and then cools down, then while running engine and remaining the transmission in PARKING position, press on the gas pedal until your engine reaches 3,000 RPM. Check if your heater blows warm/hot air. If it does, then your water pump does not work properly and should be replaced. If the air still cold, I would suggest flushing the heater core.

First you have to identify what causes the problem.
To do this you have to:
1) When engine is cold check the level of coolant. If it is low fill it up.
2) Start engine and check if engine reaches regular temperature. If your engine is not heated enough it means your thermostat does not work properly and should be replaced.
3) If engine temperature is normal, then check the temperature of pipes that go to/from heater core. These pipes are located up the fire wall (easier access is from the passenger side). If pipe/pipes are cold (even engine is warm) it means you heater core is plugged and should be flushed. Keep in mind, flushing the whole cooling system is different from flushing heater core.
4) If pipe/pipes are hot/warm, turn off the fan, switch controller to the hot position, wait for 3-4 minutes and turn on the fan. Note if the cold air blows first or warm air blows first but it cools down in 5-10 seconds. If the air blows cold than it is most probably the problem with blend door or blend door actuator.
5) If air blows warm first and then cools down, then while running engine and remaining the transmission in PARKING position, press on the gas pedal until your engine reaches 3,000 RPM. Check if your heater blows warm/hot air. If it does, then your water pump does not work properly and should be replaced. If the air still cold, I would suggest flushing the heater core.

1. Drain the engine coolant into a suitable container.
2. Open the instrument panel glove compartment. Push in on the sides of the compartment to release it, allowing access to the heater core.

The heater core can be damaged if too much force is applied to the heater core pipes during hose removal.

1. Remove the heater module screws and remove the heater module assembly cover. For vehicles equipped with A/C, remove the air conditioning evaporator temperature sensor assembly from the heater and A/C cover.
2. Remove the heater core screw and clamp.
3. Remove the hose pipe clamp screw and the hose pipe clamp. Clamp off the heater hoses.

Fig. 1: Heater hose and pipe routing-3.4L engine Fig. 2: Heater hose and pipe routing-3.8L engine Fig. 3: Heater hose and pipe routing-5.7L engine

1. Disconnect the heater hoses from the pipes.
2. Remove the heater core by carefully pulling it towards you.

Fig. 4: Exploded view of the heater core removed from the heater module assemblyTo install:

1. Install the heater core and attach the heater hose assembly to the heater hose pipes. Note the following:
   1. Lubricate the heater core pipes with petroleum jelly for ease of installation and to assure a good seal.
   2. Be sure the seals around the heater pipes remain in place when installing.
   3. To verify that the seal is installed correctly, observe the seal from inside the engine compartment. If the seal has leaks, apply a sealer between the heater core pipes and the evaporator housing.
2. Install the hose pipe clamp and the bolt/screw. Unclamp the heater hoses. Tighten the hose pipe clamp bolt/screw to 16 inch lbs. (1.8 Nm).
3. Install the heater core clamp and screw. Tighten the screw to 16 inch lbs. (1.8 Nm).
4. Install the heater module assembly cover and secure with the retaining screws. Tighten the screws to 18 inch lbs. (2 Nm).
5. Connect the negative battery cable.
6. Refill the cooling system. Operate the engine and check for leaks, add coolant if necessary.
7. Install the instrument panel glove compartment.

A- In/Out Pipe rear Heater Matrix *
B - Inlet from engine
C - Inlet to heater matrix
D- In/Out Pipe of rear heater Matrix *
E - 12v Solenoid that controls the vacuum
* I have never noticed a right and wrong way for these two as either has given me correct operation, If anyone has anything different to say feel free to inform me.