Q1: I'd suggest sewing a layer of black nylon between. Black will block any light trying to shine through the flag, and only allow light to be on the flag.
Q2: Does the nylon need to be bonded before cutting? If the nylon is being heat-bonded to the flag (I'm assuming this is the same project), I would do a test run with some scraps:
- wood board
- aluminum foil
- fabric (face-side down)
- bonding material (interfacing?)
- a layer of wax paper and/or another of aluminum foil
- top it off with a wet rag
and iron that fabric sandwich.
- The wood will keep everything still and help prevent slips or stretches
- The wood and foil should help keep the heat localized
- The layer above the adhesive should be something easily removable, like pulling a sticker off it's original waxy paper
- If using another layer of foil, it'll again just help direct that heat to whatever is under the foil
- The wet cloth is important, and perhaps keep some extra water handy -- heated water will not go above 212F, so as long as the cloth is wet, that's going to be the highest temperature you should be able to use. Most interfacing should melt at this temperature.
If you're bonding nylon to nylon, just make sure that wherever you have exposed heat-bonding stuff you keep it covered with wax paper or something like that.
Oh, and if you're avoiding sewing altogether, just use the same heat-bonding stuff around the edges of the inside part of the overall flag. You could take the black nylon, cut it to the same shape as the other two faces of the flag, then heat-bond one face to the liner at the edges, then do a second round of heat-bonding (I'd suggest two separate ironings for this, you wouldn't want one face to only partially bond because it didn't get enough heat for the glue to melt)