Though I'm not sure if I understood all of your questions
correctly I'll try to answer them best I can:
Scripts on a frame run once everytime the "playhead" of it's
timeline enters the frame. It is ran again everytime the frame is
enterad again - e.g. with loops or scripts ("gotoAndPlay")
Each mc has it's own independent timeline. Stopping the main
timeline (or any other) won't affect your mc's timeline and
therfore the answer is: Yes it will.
The answer to your second question is also "yes". In fact
when you have an mc called "my_mc" on the stage and make a new
keyframe, that is what Flash does - more or less.
But be carefull when doing it manually, and don't do it if