Just did this on my 02 with the manual windows.
After you take the door panel off there are 2 black clips with teeth which are each held on by 1 10mm (I think, don't hold it to me here) bolt which tightens the clip onto the window. The one at the back of the door is easy to get to, but the one at the front is damn near impossible.
Basically just loosen the black clip and shove the window in it and do your best to get the front in. I did mine 2 months ago and its still holding strong. If it pops out I'll most likely glue it too!
Half my posts are from my mobile; expect spelling mistakes
02 Dakota Sport, 3.9L, 4x4, 3 inch Body Lift, 31x10.5.x15 Wranglers, A.R.E Tonneau Cover, 20% Tint All Around, Atlantic Blue, Kicker CVT10-2 Sub, Sound Ordnance M1500 Amp, Kicker KS60 Speakers