I used to have 2000 Sonoma extended cab. If you have a removable faceplate, just put the main body of the radio somewhere in the back. It'll take a little longer to steal that way. But don't put it under the seat, it will get too hot there. Anyway, you can mount the faceplate on top of the dash on the hard plastic just above the center A/C vents, under the ashtray, or if you want to get really creative, on top of the rear-view mirror. Galls, www.galls.com
, has some pretty neat mounting solutions for transmission humps. All the cops use 'em, so they're tough too.
About routing the power cable, you have several options. The first is the hole where the clutch pedal would have been if you had a stick, the second is one of the plugs underneath the sills on either side of the truck, the third is the hole where the stereo antenna lead comes inside. Also, this goes without saying, but run both positive and negative wires from the battery, both fused. It will save you a lot of hassle later with grounding problems, noise, and blown fuses.
It will be very hard to see the spots in the "firewall", and you don't want to drill into a heater hose or your master cylinder, so be careful. If you've never done it before, consider a two-way radio shop that installs in cars, preferably places that service police and other public safety. Ham radios aren't that different, and chances are there will be a ham there too. One more thing, I used a simple mag-mount 5/8 wave on one of the wheelwells in the bed. It probably wasn't the ideal place to put it, but I usually had pretty good reception and reports with it. Good luck!