110% install the headliner before you put the glass in, especially since you already have the glass out. IMO, it's not even a choice.
413, I'm not sure what cars you've done them on but based on my experience, putting a bow/cloth style headliner in a Duster with the glass in sucks. It can be done (I did it on my own Duster) but it's not easy (especially on your back) and the results will not be as good.
Unless I'm missing something, it's physically impossible to get the headliner material evenly on the hooks around the window opening with the glass in. I tried to do it that way and ended up making a mess of my brand new headliner. What happens is you end up just stuffing the material in between the window edge and weatherstripping. When you go to trim it, it will be too long in some places and too short in others and/or it will rip.
To get it wrinkle-free the material needs to be pulled tight on the hooks around the rear window opening - that's what they're there for. Once it's straight and even on both sides, you work forward pulling the material tight to the sides until you get to the windshield. Have to pull the sail panels and plastic trim out as well at least on pre-'72 models with bow headliners. Make sure not to lose the little clips that hold the material to the upper window channel, I think there are 2-3 on each side.
Make sure to glue it down (with general automotive adhesive) along the hidden edges where the hooks and clips are and then trim any excess. You want it as neat as possible in those areas so the trim goes back on easily and there's no holes showing or extra material hanging out.
Also, make 100% sure the job is to your liking before you locate and install the visors, mirror, dome light etc. as there's no more adjustment once you make a hole in the material.
