Ok, now what's the best way to put them back in place?

 

I would either r&r the window or use some Window Weld .. its a sealent thats used by factorys to install windshields and side glass..

Dont be tempted to use silicone of any kind .. UV will break it down real fast IF it will even stick .. been there ..

 

Duct tape . If the seal is leaking there is a chance it will need to be replaced, they are not crazy money and the R&R of the window is your best bet.

 

Forgive my ignorance but r&r of a window? Is That remove and replace?

 

I was getting in from my third brake light, but it wasn't finding it's way all the way to the front floorboards.

 

Yes , Remove and replace seal .. not window ..