Some guesswork here, but the top F-1X has the two power outs. Then there's a jumper cable from jack #2 on the top one, to #1 on the bottom one - so that's probably how the bottom F-1X gets its signal.
Assuming he's running the pickups into separate channels, there could be internal wiring to route one pickup signal to jack #2 (though I would hazard a guess that you can always run a jumper cable from the second jack, like on a two-channel Marshall head).
The switch just above jack #2 could select the instrument input, or the pickup to be routed to the other F-1X.