Headunit: Get the wiring harness adapter like this one.
http://www.crutchfield.com/S-SHtzhFg...00&I=120701761
Also found at Autozone for the same price.
You take this adapter and solder the labeled wires to the aftermarket headunits wiring harness. You do this out of the car on your workbench

When it comes time to install the headunit into the truck you just connect it to the factory wiring connetor.
Now is also a good time to install your PAC SWIX unit if you have steering wheel controls.
They make brand specific connectors too so you don't have to mount the remote eye laser thing.
http://www.crutchfield.com/S-SHtzhFg...Dps&i=127SWIPS
That one is for Sony and Pioneer.
If you are using amps, you will need to route RCA's from the back of the headunit to the amps. You always want to wire the RCA's on the opposite side of the truck as the power wire for the amps. I run the RCA's through the back of the glovebox area under the dash, using zip ties to keep them up and out of site. From the back of the glovebox area route the RCA's behind the kickpanels and under the door sills. To do this pop off the door sills and then take off the black round connector on the kickpanels near the floor.
The remote turn on lead(blue wire) can run along the RCA's.
The power wire runs along the left side of the truck.
Speaker wires run from the amps to the speakers along the door sills, into the kickpanels and through the rubber grommet in the doors.
This page goes indepth about wiring speakers and deadening the doors.
http://www.toyotanation.com/forum/t120095-7.html
Crossover and gain setting.
For the interior speaker amps you should set it to HPF at around 60hz to 80hz, and not much higher at all. I prefer a 60hz crossover point for my mids.
For the subs set the low pass filter(LPF) to 60 to 80hz.
For subs I usually like to let them play a little of the midbass kick as well depending on how strong my front mids are, so usually it's set to 80hz.
Start with the gain at minimum and bring the volume on the deck to almost full level, say 90 percent. Slowly raise the gain until it is loud and clear with no distortion, then back off just a little.