Eventually you'll get a lucky roll and hit them. The rebels have a huge advantage in running missions, as they have more characters, possesions, and other advantages. So they will succeed in turning planets against you and starting rebellions. By the mid-game, you should have every one in the conterset on the board. Line units are too slow to be useful, and Patrol units are almost totally useless except as decoys.
Elites are great but expensive.
In general, keep your troops in the orbit box. Only fight on the ground when you have overwhelming force. Troops on the ground are vulnerable to sabotage and assassination, not to mention the fact that rebel troops usually get 1 or 2 favorable shifts for terrain. Your troops are generally better in space, plus, units in the orbit box give you favorable modifiers for detection and may be able to blow up rebel spaceships as they move. Capitals, home planets, and important secrets.