The key to protecting yourself from the enemy is to see him before he sees you, so if you do not yet have it, get "Eyes of the Universe" (can be built after researching the last sensor tech). If you have only one ship to defend a planet then place it in orbit (ships in orbit get an attack bonus); otherwise, create a fleet from your ships and park them near your star systems. Each fast fleets with EotU should be able to protect multiple planets by intercepting incoming enemy fleets. In case the enemy transports get past your ships, you will want to build up your soldiering; research the planet invansion branch plus I think the planet defense branch, and build the Tri- Training Center.