i would never, ever use the emperor in combat. way too risky. if he dies it's game over(at least in MP campaign, havn't played single too much). he'll always sit behind a shield and a couple AT-AT's, and preferably on a world like dagobah, where you can't see he's there from orbit
boba's way too valuable to me in space, i don't even use him on land. the ability to cripple an entire wing of y-wings in one keystroke far outweighs taking out a hero for a few minutes. i feel naked w/o boba in my main fleet
definitely a good idea to keep every world garrisoned. TIE maulers are cheap, fast, and make road kill of hordes of PLEX. shield generators on every world is a must, even if you have to sell off a structure to make room. just make sure to research stutter shields so rebel artillery can't fire through it.
but a few squads of storm troopers(or an AT-AT if you can afford it) is also a good idea, to "capture", and build on any turret spots.