This is a great topic, electricals are a MAJOR source of headaches on modified vehicles and can ruin an expedition. Twice I've been on trips where an electrical glitch caused a fire. One of these was minor and we could patch the truck up to return to civilization, the other one resulted in a full-blown fire that not only consumed the truck but also all of the gear/equipment in it, the driver and copilot barely had time to get out. We were several hundred miles of rough trails away from the nearest town and had a guy with 2nd degree burns, not to mention having to pack people into trucks that we'd originally planned to carry only two folks (mine didn't even have a back seat at the time).
I've always found interesting that so many people (and I don't complete exonerate myself from this) spend thousands of dollars on their rigs and accessories, then use subpar connectors or just do a quickie install.
My first suggestion is to get yourself a dedicated second fusebox. Prices and sources vary wildly, but there's something out there for every budget. Ideally, the second fusebox should be mounted on dry, easily-accessible location, either inside, or high up on the engine compartment. If you can't swing one of the weather-proof models, buy a nice-quality tupperware (not the disposable ones) with a good sealing lid and mount it to the firewall or inner fenderwell, with the fusebox inside it and all cables run through holes on the tupperware, then sealed with good quality silicone. One neat feature of using the tupperware is that you can stick a diagram of the fusebox inside the lid (after laminating it).
Another suggestion is the use of a relay bank. You can get a perforated steel flat stock (galvanized) at any of the DIY warehouses, and you can buy relay plugs from www.partsexpress.com/ for cheap. These plugs make it a LOT easier to connect relays to your accessories. The perforated flat stock is a perfect mount for a row of relays, that way you have them all together and easily accessible. You can even mount a couple of spare ones to the bank and cover the connectors with an unused relay plug.
Once you have your accessory wiring harness mapped out, it's time to buy cable. Do yourself a favor, get good quality cable of the right gauge. Don't go overboard, you don't need welder wires to connect a couple of rocklights, but at the same time, don't use the skinny, low-quality stuff that comes with the lights. And while it may be more expensive, BUY different color wires for each accessory!!!! There's nothing worse than having to use a tester over and over to identify the right wire for an connection, especially since these things tend to happen on the side of the road, in the dark/rain/etc... If you can't afford to buy different color wire, at least make sure you label the wires at each end.
Ditto for the connectors, get the good quality stuff and make sure you use a tiny dab of dielectric grease to prevent short-circuiting from corrosion.
I am a HUGE fan of shrink-tubing, especially the marine kind that has the adhesive on the inside. It creates an excellent seal and the installation looks a lot cleaner than using electrical tape (which retains moisture, unravels in hot climates, and creates a sticky mess). For certain connections, it pays to solder the connector first, then use shrink tubing over it. This may sound like overkill, but if you expect any vibration, it's best to take the extra step and not have to deal with a broken-off connector later.
If you have a second battery (and I highly recommend this for expedition use), route most of your accessories to this battery, so you don't place undue tax on your main (starter battery). There might be a few crucial accessories that you might want to route to the main battery, but for the most part, use the auxiliary battery.
If you're going to route wires through the firewall, use good quality silicone grommets (also available through the link above) and try to match the diameter of the grommets to make the seal as tight as possible. If you can't, then consider sealing the grommet with clear silicone, especially if you're in a wet climate, moisture can get through into the interior.
Once you have your wiring harness in place and you've run all the cables, clean them up with a LOT of nylon zip ties and pack them into wiring loom. There's nothing worse than opening up an engine compartment and finding a spaghetti bowl of wires going in every direction! Besides, loom will protect the wires from abrasion and heat and slung mud. If you're going to route wires to the back of the truck and want to do so along the frame, you might want to consider substituting the wire loom for a wider diameter rubber hose. It's a PITA to run the wires through it, but it will protect them better from the elements.
Use smaller sections of rubber hose on your loom (split it down the middle, then wrap it around your loom and zip tie it back together) where it touches the metal, gets close to the engine or radiator or anywhere you fear abrasion/contact.
Finally, get yourself one of those clear tackle boxes with multiple compartments and make sure you fill it with spare fuses, fuse plugs, connectors, splicers, shrink tubing, relays, zip ties and bulbs. Add a good quality crimping/stripping tool, a good quality tester, a couple of spare switches, a small tube of dielectric grease, soldering wire, a small can of WD40 and a small stiff wire brush to clean connectors and/or ground spots. Top it off with enough extra wire (go overkill on the guage so you can cover multiple installations) to go from one end of your rig to the other at least once).This is the beginning of a good electrical tool kit that is guaranteed to make your life (and those who travel with you) a lot easier.
The above applies not only to accessory wiring, but for those of you that like me, driving older rigs for expedition use, it applies also to replacement wiring. Many of the OEM connectors on older rigs, especially in the engine compartment, can be brittle and in need of replacement, and even wire insulation can get stiff and break off. Go through your engine compartment, starting with the key components (like the starter, the coil, the headlights) and check to see the condition of the wiring. If anything looks hokey, go ahead and replace it now, don't wait until it fails because Muprhy's Law dictates it will happen on that dream trip to Baja instead of on that lazy Sunday right after the Super Bowl.
This write-up is condensed from one of the chapters of my revised "Guide to Expeditions", hope it helps.
Editor, South & Central America
'99 UZJ100 Toyota Land Cruiser