The headliner wraps around the flange of the rear window, so it has to go in forst, then install the window. In the front, there should be a strip pop riveted to the hardtop just above, (when the top is upright), where the clamps mount. The headliner wraps around this. So what that means is it needs to come off. What I've done is to lay the headliner in the top with a couple of the bows in to mark position. Then lay the strip in place over top and mark with chalk or a pencil where the front of the fabric would wrap around the front of the strip. Remove and fold the fabric over the front edge of the top. Lay the strip in place and re rivet, while lining up the markes with the front of the strip and the fabric trapped between the strip and the top. This means folding it back and forth as you go since the marks are on the other side. Once the strip is fastened down, fold the headliner back in place and install the bows into it and the holes in the top. Pull tight and wrap around the rear window flange. I find it works best to use som small strips of wood and clamps to hold it in place while the glue dries there. The install the window.
As for the quarter windows, there should be a seal on the flange of the top for them if you don't have that.