I'm probably not the best source on the solenoid, but I've given enough thought to this that I'd hope I understand. My guess is that you would wire it in-line with either of the positive battery cables from the perko, and it should work fine when the perko is in the "all" position. I could be wrong though, I'm a rookie. My other hunch is that amplifiers should both be hooked up to the same battery. It probably doesn't matter with a Perko, but with an isolator it would draw from both (or possibly neither?) battery when the boat isn't running.
As to my system, the battery install is done and the tower speakers wires are all run. All wiring is wrapped in the insulator tubing, which makes it look very nice, especially for the wiring exposed at the tower speakers. I tracked down some audiosource 14-ga round 4-conducter wiring and used that instead, which was much easier to work with than the traditional flat speaker wire. Fit through the tower-base fiberglass hole easily. And the shop-vac trick works like a charm.
For anybody trying to do this utilizing the stock Bose tower speaker holes (as I did), here are two tips: 1) in the base of the tower, it is easiest to wire UP the tube...from the boat to the hinge on the tower. 2) for the tower itself, wire DOWN from the speaker locations to the tower-base/hinge. Yes, you will have to splice, which I really did not want to do. But I spent probably two hours wasting my time trying to get wires to round the corners through the cross-bars that they simply would not do. So I gave up and spliced REALLY well, then tucked the wiring way up into the tower so that it shouldn't be disturbed.
Everything is installed -- just waiting on an amp-board that is being cut and carpeted by a local shop (too lazy to do it myself, they said they'd do it for $10), then the amps go in and I get to fire 'er up! I'll post pics when I get it out of the garage in a couple weeks.