This is something i have been trying to learn also. As i dont like to sacrifice my ships for a small bonus, then haveing to re deploy my ships back to there planet.
The couple of things i do is when i get to the point where i have enough of an income, look and see what planet your aly is always attacking. Help them take that planet over. this will give you another place to put a ship to get relations higher. If the planet isnt connected to there planet, they wont take it. At this point, you may have to babysit the planet to help them keep it.
I am not an expert at the game, i am hoping for mors suggestions here also. Besides the obvious, give them crystal upgrade.