I wired my 14 ft. aluminum boat about ten years ago. I'm no electrician by any means, but all my lights and gadgets still work and they've never crapped out on me. I decided to use two separate 12 volt batteries - one for the electric motor and one for the lights and electronics. I mounted a plastic battery box to the plywood floor near the stern where I connect my trolling motor using a quick connect that I added to the motor wires. I also have a 50 or 60 amp trolling motor fuse connected to the quick connect wires on the battery side that I leave connected to the battery at all times. Put the battery in the box, strap the lid in place, plug the two quick connect ends together and done.
The second battery box is mounted to the plywood floor between the first and second row of seats along the side. I figured this would help distribute some of the weight of having two batteries. On the second battery I run my navigation light, anchor light, bilge pump, fish finder and a four or five foot long thin strip of LED lights pasted under the gunwale that light up most of the entire inside of the boat. These lights are too bright while out fishing, but they're great when it's time to unload the boat in the dark.
I connected all of the lights and gadgets to a marine switch panel. I connected the battery power (positive) to the switch using EPM 10/2 boat cable. It looks like residential ROMEX wire, but inside the white outer covering there is a separate marine grade red wire and black wire. I have ring terminal connectors and a 40 amp fuse on this end of the 10/2 cable, so I just put the battery in the box and connect the terminals to the battery posts with wing nuts and everything has power. I ran the 10/2 boat cable from the battery back to near my tank seat at the stern. The marine switch I used is designed to be fitted into a console, which my boat does not have. It's just a utility semi-v with three rows of tank seats. I bought a weatherproof "polybox" of the appropriate size to house the switch and cut out an opening in the top cover of the box and mounted the switch into the box. I have the box mounted to the third tank seat at the stern, so the switches are all within my reach. The switch panel also has a 12-volt power outlet, which comes in handy for things like submersible fishing lights, spotlights, etc.
At the top corner of the wood transom just behind the seat where the switch panel is located, I mounted a tinned copper bus bar (terminal block) with multiple connection points (i.e. philips head screws to accept ring connectors). The bus bar collects and connects all of the grounds back to a single source. The negative wire from the battery (10/2 boat cable) is also connected to the bus bar. All of the 16 or 18 gauge negative (black) wires from the lights and gadgets are run directly to the bus bar and connected and grounded there, which is grounded back to the battery through the 10/2 cable. All of the positive (red) 16 or 18 AWG tinned copper marine wire running from the lights and gadgets go into the switch panel for power.
The switch panel contains fuses for each switch, so everything is run through an appropriate size fuse. If I remember correctly, the switch panel uses male blade-type connectors, so I needed female terminals to connect wires to the individual switches in the panel. At the moment, I don't remember why, but I also needed a three-way connector inside the switch box for something. It might have been to connect the main power from the battery to the switch panel. That connector might've been included with the switch panel. I ran all wires through plastic wire loom wherever possible for added protection and used cable/wire ties and organizers to keep it all tidy. Also, when I purchased the marine wire, I made sure to purchase all of the correctly sized marine grade ring terminal connectors, spade terminal connectors, etc. with heat shrink collars attached. I can't remember the online store where I purchased the tinned copper marine grade wire, boat cable and connectors; however, I do remember it was a no-frills online store that specialized in only this stuff and was MUCH cheaper than buying at a place like Cabela's, West Marine or Bass Pro.
This is similar to the switch panel I used:
Seasense Switch PanelI can't find a link to the polybox I used to mount the switch panel. I felt stupid buying it at the time because I think I paid more for the empty plastic box than I did for the switch panel. It was some sort of industrial/scientific grade plastic box with a rubber-gasketed lid. It's slightly smaller than two boxes of shotgun shells placed side-by-side. In addition to making a cut out in the lid to mount the switch panel, I drilled a hole in one side to run the positive cable and positive wires into it then just caulked it tight.
Sorry for not adding pics. I quit photos after Photobucket puked.