To answer part of your question directly - yes, you can use each handle of the Z4K separately to power each half of the layout with one handle going to Fixed 1 and out to a distribution panel and the other handle to Fixed 2 and out to a second distribution panel. The 45 ft. length, in itself, should not create a signal issue. I would go with the 12 gauge if you are starting from scratch. If you had a lot of extra 14 gauge laying around, I would try that first.
As far as going up and over two doors, have you considered pulling up that section of carpet and running the wiring underneath or even on top of the carpet under a vinyl/rubber/plastic protector ?
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