For advice like "Stay away from Brand X", it would be useful to state why. I worked for several years as an audio amplifier repair technician and modern audio amplifiers are very much cookie-cutter devices, where one is much like another. There *are* reasons to stay away from certain brands, as some have absolutely horrible build quality using very *very* cheap quality parts and construction, and blatantly lie on the packaging about the power and noise specifications. At the other end of the spectrum some are made to well beyond military-grade specifications, are conservatively rated, and command top-dollar. I do recommend sticking with quality name brands. I have all Alpine amplifiers in my car and I'm very happy with those.
The inner door panels come off relatively easily if you know where the mounting bolts and the plastic fasteners are. Remove the bolts and carefully pry around the edges at the fasteners with a trim removal pry-tool and you shouldn't have any problems.
Wiring a trunk amp to the door speakers can be done a couple of ways. There is a cheap installer shortcut that many installers use. Presume for the sake of example that you put a 4-channel amp in the trunk. You run new speaker wires directly from the amp to the rear speakers, since they're all right there in the trunk. Then you re-use the factory rear speaker wires in reverse, by connecting the ends that used to go to the rear speakers to the amplifier's *front* speaker *outputs*, and up at the dashboard at the radio wiring harness you *disconnect* both the door and rear speaker wires and connect them together so the left rear wires are joined to the left door speaker wires and the right rear wires are joined to the right door speaker wires. I have a diagram of that somewhere, if I can find it I'll post it. [Edit: Here you go:]
The other way is to run new speaker wires from the trunk up the wiring harness channels under the door sills up to the footwell kickplates and up through the wiring harness sheaths into the door. I've done that too, and on your year Bonneville that's not a terribly difficult job either. [Edit: My current system, red and black wires are line-outputs from the head unit, blue and green wires are speaker wires:]

PontiacDad at WCBF `08: "By any chance, was his name. . .Radomir?"
R.I.P. 10/31/15: 1997 SE: "Silver Shadow"
`05 Mercedes S500