Generally, from what I've seen, when your ships jump into a grav well, the carriers sit back on the edges a good bit of the time, while the fighters/bombers do the dirty work, so the short answer to #1 is "no."
You can select all fighters or bombers in a grav well by holding the alt key, then clicking on any squadron.
As far as what I can remember, there is no, "guard command" for any unit in the game, though it would be useful if there were!