glass windows at the rear on the sides of the roof whats the best way to seal these up as they leak when it rains.

 

Are you talking about the side windows or the Alpine glass.
On the top, Alpine windows, if they are not leaking too bad you might try some silicone sealant. Same on the side window except if they are cracking too much. If there is much cracking replace the seal so you don't get some long term leakage and then rust or rot.
Mike