Help adjusting quarter windows

Just put mine in , don't have the doors on yet but it seems to go up to the new top rubber ok, but does not seem to go into the rubber gap as much as one would think it should, spent over half a day messing with adjustments on driver side, right side went better (64 cuda) Great does that mean more adjusting when the doors go on? They both slide up to the same rubber channel ! Redfish you are right don't take them out if you don't have to!!!