I N EED TO KNOW HOW TO CLEAN THE DRAINS IN THE SUNROOF

Make sure the sunroof water drains are clear, they are at the corners of the open sunroof in the body structure, the roof is not designed water tight, it depends on the water drains to keep from leaking

Here is a link to a exploded view . http://parts.tubmanchev.com/a/48127815__6013728/ROOF--SUNROOF/BC05450.html
You can easily run some trimmer line up your drains from the bottom up to keep them clear. ROOF SUNROOF Fits STS 3 6L V6 Automatic Base STS 3 6L V6 Automatic...

Does it have a sunroof? Open your sunroof and clean out the drain and channels around it. Probably dirty letting water spill out into your car.

Remove the drive motor and gear assembly from the roof and close the top, then reinstall it.

The beetle has also been recalled for a sunroof issue, I found this website:-

http://newbeetle.org/forums/questions-issues-concerns-problems-new-beetle/43357-new-sunroof-recall.html

Where it says:-

"Sorry if I put this in the wrong place but I just got a recall notice for the sunroof drains on my bug.
It's SERVICE ACTION 60A7/S9 and pertains to all NBs from 2001 - 2007 equipped with sunroofs. It's also for certain Jettas, Audi A4s, Golfs, GTI, and Passats. You'll probably get a notice but I wanted to let people know just in case, for some reason, they don't get the notification...maybe because they're not an original owner etc.

VW will clean, modify and inspect the sunroof drains and tubes. There's also a form to be reimbursed if you've had to pay for any problems in the past".

Which means that, if you or your car didn't go to this recall, then VW will sort it all out for you for for free. Its a manufacturer's problem.

Just pop in to a dealership and ask, if its been done, you're back to square one but its worth a crack................. Good Luck.

However, here's a website which shows you how to service your sunroof.

http://www.ehow.com/how_4508388_service-sun-roof-vw-beetle.html
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the drain holes are located at each corner of the sun roof carrier. you will need to open the sun roof all the way to be able to see the drain holes. the drain pipes run down the A and C posts of the vehicle. [A post front] [C post rear]. the easiest way to clear them is to use a flexible piece of cable pushed down from the top. if they are not blocked, the pipes may be off on the under side of the sun roof carrier. this usually happens if somebody has been doing panel work on the vehicle and forget to reconnect pipes. to rectify this you will have to lower roof lining. pipes just push on.

Check the sunroof drains. The vapor panels are hard to make stick. We used to use hot glue and duct tape to help hold on the vapor panals. Check the drains in the doors.

If the actual seals around the sunroof are okay, you may need to clean out the drains. These drains usually follow down the a-pillars and dump underneath the car. The sunroof will always get water in it, and that's why it has drains. Over time, these drains get clogged with dirt and leaves, etc. and back up. With nowhere else to go, the water will leak right into the car. This problem is better dealt with by a mechanic with some experience, but if you can get to the drains, either by removing the headliner or removing the sunroof glass, you can blow them out with compressed air, or if that doesn't work, run a long wire through them, just be careful not to puncture the drains (they're usually rubber or plastic tubing) as this will cause another, harder-to-fix leak.

Good Luck, hope this helps!

pull up our dash. push your center dash forward push with force will pop forward remove bolts size torx 25 that is it tip size for your wrench remove the plastic covers will reveal another plastic piece as well. there you will find you ecm DO NOT DISCONNECT. ecm pull up there is a square cover this is where your wire connectors are. pull that up. clean all debris that you can. make sure area is dry.use a white silicone sealant for automotive seal cover put back on and reinstall in reverse order. good luck