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.. :c:

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

Duct tape lol. 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 .. :c: