There are different ways to manage fleets.  If you are breaking into a hostile gravity well with mines, heavy defenses, and a starbase, I suggest you have your entire fleet in "hold position" and you manually control their movement.

After repulsing a big AI fleet and weakening them enough to start an offensive, take a corner of the enemy gravwell and let them come to you.  Use your firepower and flak defensively while using bombers to pick apart the defensive positions.  Have scouts with your fleet so as you inch forward, your fleet destroys the mines that the scouts detect.  If you think you will get overrun by newly built reinforcements, construct your own starbase to hold your corner of the gravwell and keep your fleet by it.

Eventually you will destroy enough defenses and ships that your fleet will be free to assault the enemy starbase and then take the world.  You will have to inch forward world by world this way until the AI finally doesn't have the econ to support a defense and you start to steamroll.

The main thing is try to fight defensively, even in the enemy gravwell, and not let your ships run around and get picked off by defenses.