In general aircraft canopy frames are painted and finished the same as the rest of the craft, so they need to be exposed to all your spraying and weathering and such right to the end, until finally the masks come off.
Now the very best way to mask the glazing is to find a die cut mask set. you might get lucky.

Failing that, you need a roll of narrow Tamiya masking tape and a sharp pair of little scissors, and carefully cut and place overlapping strips along the edges of the frames. you can get fancy and use hole punches to make inside corner radius bits. This is tedious work, no way around it. once youve gone around all the edges and firmly burnished them down to prevent leakage, then you can thoroughly tape over the rest of the glass area.

I havent ever used the Future floor polish myself, I know people apply it to clear styrene to give a bright shine. if thats the intent I suppose youd apply it first to frames and all and let it harden, before doing any masking, and you can paint right on top of it on the exposed frames.