Not sure if they are related but the front sun roof is very noisy when opened and leaks ALOT.

When opened it bangs a lot one each little pothole. The rear sunroof does not do the same, so it must have something wrong with it. Also, it leaks a lot...

how do I check the drain? do I need to remove the roof lining?

It is an electrical sun roof by the way...

 

Sunroofs have been covered dozens of times on this forum. Start by looking in the section for your truck (whatever it is -- you don't say what you have) and using the search function.