First thing I would do is dip all the clear parts in Future. This will protect the part from scratches and other mishaps the may occur. plus it give the masking material a smooth surface to adhere to.
After the Future dries. I usually mask all the clear parts first with whatever masking material I am using. Low tack tape, photo frisket, blue tack,etc.Then test fit the piece to see if I may have any problems removing the mask once painted.
I then cut out whatever framing I need to cut while the glass is off the model. It is easier for me to do this while holding it in my hand rather than it being mounted.
Test fit it one more time to check the fit and masking to make sure everything in ok. Once satisfied with the second test fit I mount the glass perminantly where it is suppose to go.
Once the model is constructed, painted, weathered dull coated,etc I the remove to masks.(usually it is the last thing I remove from the model) Any residue that may stay on the glass can easily and gently be removed with some rubbing alcohol and a cotton swab.Without damaging the Future.
Hope this helps and makes some sense. Good luck and hope to see some pictures.