i posted some info & pics on the soffseal t top weatherstrips awhile back but cant seem to find it now. heres what i found dealing with the seals available today. the soffseals are the best option for seals right now aside from finding NOS ones or good original ones. they are a little thick but will compress some over time, but for new seals you almost always have to adjust the metal receiver tabs to make it easier for the tops to latch.
compared to the metro brand the soffseals are far better for fitment & designed more like the originals, the metros are flimsy & dont conform to the corners at all, they leave a big gap to the roof line for water/debris to get in. i returned 2 sets of them once i saw how they fit.
the soffseals should definitely not be flush with the roof, they should be set down in the channel somewhat, about 1/8". if you can get to the metal blocks they need to be backed off a tad which will allow the t top rod to engage & latch. but dont go too far or the tops will leak/rattle if adjusted too loose.
another trick i did to really help the seals is to coat them with a good rubber/vinyl treatment like meguires... not armor all. then, if/when the car will be sitting for awhile i put some weight on the tops to help speed up compressing the seals. actuallly quite a bit of weight, like 40-60 lbs, i used some steel rally 2 rims i had , lay the edge of the rim or weight right at the metal edge of the t tops for some added support so the weights not resting on just the glass, i put a sheet or piece of thick cardboard to protect the tops. i do this when the car sits for winter storage so its like 2-3 months... but it definitely helped the tops settle down into the seals & made latching them much easier compared to when they were new. its kind of like new door seals etc, the first time closing the doors is usually terrible but it gets much better after a week or 2 as the seals form.
main thing is to adjust the metal tabs correctly for the new thick seals, then use some weight to speed up the compression. then, if teh tops are too loose after awhile you can readjust the tabs. they will get better & be able to latch with some help & time.