1) Wire to the house battery, never to the starter.
2) Best is to wire after the house battery switch so when the house is switched off the down rigger outlets are not energized. You can wire directly, but your downriggers will always be "on".
3) Several different types of fuses you can use. You can do a simple inline fuse, which is probably simplest, but least preferable. If you have a central location where you can mount on a vertical surface, a fuse block is better.
4) Use the largest wire you can Scotty recommends 12 Ga, or 10 Ga for longer runs, but you can go up to 8 Ga in the Marinco plugs. Especially if you are going to use an Ace puller as they take a 40 amp fuse which requires 8 Ga wire.