In reply to:

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Another way of handling it would be to wire BOTH units directly to the amplifier via an A/B switch of some kind

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EEEK!!
Unless you ran RCA to split leads, then the switch. then lead to RCA connectors, ouch!, that would probably bring in a lot of noice, switches are not exacly the most shielded of units. Plus, I am pretty sure any solder or whatever used to fashion this together would introduce all sorts of clipping an frequency loss (I could be wrong, but I guess if it is ok for digital signals, then analogue couldnt hurt - too much, I dont want to get into an argument about waveform clipping and distortion, so yes, digital signals are easier to "reconstruct")
But back to switches, well, you could try it out on the bench, before you put blood, sweat and tears into the auto, and see if it's possible.
But for amp remote switching, you would have to introduce another switch (imagine an inverted Y, head units onm the bottom, amp at top, switch in middle), and while +12VDC isnt anything to scream about, I am sure them amp would function fairly well with that switch in the middle.
But ask a shop, or tanstaafl might help, if he reads this. He might have some insight into this.

Best bet would be to wire the Empeg into the aux of the other head unit (unless that aux isnt taken up by some changer unit)

Or get two amps...
With 4 more speakers...
And another two subs...
And see which system wins!!!
(Obviously I am kidding here, but for that install, well, lets just say you would need a big alternator, and a large SUV to ferry that all around in)
IASCA would have a field day with that install

Smoker_Man
#080000449 MkII - 36Gb Blue