Side Widow Glass Alignment Issues

New to this so please be patient, just picked up a 66 coupe pretty tidy overall and have started fixing a few minor problems. Thought I'd tackle the damaged/patched up quarter window glass seals that meet up to the back edge of door glass, got a pair of Drake window seals and replaced the old ones. But found they don't do the job as the glass is clearly out of alignment, looked on the net and it appears to be a common problem. Could anyone please talk me through how to do the adjustments to make it seal. Thanks in advance for any help.

Well today I learnt the art of adjusting the side glass in my 66 coupe, it had patched up seals when I got it so I brought a new pair and put them in.................it wasn't fit and forget. Fortunately I've got a friend who lives an hour away who works on early Mustangs usually setting them up for racing. We took out the back seat, side trims and front door panels and Rick adjusted the front quarter windows, door glass then lastly the back quarter windows. What a fiddly job, adjust check adjust again and again and the end result was great. we achieved a good seal on both windows.Pics from the outside are the final adjustments finished. Thanks Rick for your time and it's good to know there are people out there who are willing to share their knowledge