I'd like to add one little thing to the manual landing portion though: Since many time you'll be landing straight out of combat, or with mere seconds before FTL, you'll frequently be coming in too fast to make it pretty. Use reverse thrust to slow down and avoid over-shooting the landing pad, which could happen if you just kill your engines.
And yes, that did happen to me once before I remembered that I had reverse thrust. I flew in too fast, bounced off the deck a few times, and shot out the other side. Had to make a U-turn.