Do FFCs have any built in flags (bools or ints, doesn't matter)? And if so, what exactly is the process for setting them up (if need be)?
Unless there is another way to have an FFC run exactly once per game file.
Run Once Flags?
No, this is impossible to do!!
...Okay, I lied. You can use either
1) screen D[] variables, or
2) a global variable. (Or a global array)
Either one get's saved in the save file. Personally I would just use a global array if these scripts are sparse.
Well, as for Boss intro sequences, I suppose the Screen D[] would work. Nice, this will help in a lot of places.
If it has to do with just one screen I usually use Screen->D. It's very useful for keeping track of what's been done on screen. I know a few scripts have used it for screen secrets, locks, a rupee room that remembers what rupees have been picked up, etc.