I have a dual bus system complete with dual alternator, dual battery. How much support does the AFS-5000 series have for such a set up?

Dual bus is not uncommon in Lancairs at least, and almost mandatory (in my view) if you have an all-electric panel.

AFAIK, the engine management module only shows a single voltage and amperage. This is a step down from the MVP50 I had, which supported dual bus (although poorly).

I don't have the free connectors (or the cash) to get a VP-X Pro (which supports dual bus I think), but even I'm not sure the AFS would allow me to monitor both buses.