Are they in parallell or series?
Good point. You should put them beside each other in 2 separate audio pathways, and then Y them back together into the same cabinet, or actually (and this is how I do it) - put amp 2 and cab 2 in parallel below amp 1 and cab 1, and Y the audio back together AFTER the cab 2 output, back into the main signal path. if you don't understand what I mean, go to the Fractal Axe-Edit page (you know the one I check everyday, hoping to find the link for Axe Edit download) and look at the banner photo. There is a signal chain on pathway 2, and there is a second amp and cabinet on pathway 3, that is split off before the amps, and recombined together after the cabinets - this is how I do it. Incidentally, I also side chain my delays and my reverbs every time like this. It makes my presets a lot louder too.
I started using a 2nd amp in mid-December. I do not run them at the same time. I had to set up a modifier to select Amp1 or Amp2. I actually set up the modifier to engage the MUTE feature of both amps, but on amp 2, I reversed the sweep of the modifier. So if you pictured a volume pedal, instead of a push button switch, you could imagine that amp1 turns on when I step on the volume toe down, and off when I step on it heel down. Amp 2 is the exact opposite - amp 2 turns off with the toe down, and on with the heel down. Therefore, to control/select my amps, my MIDI controller is toggling that modifier to mute the amps, out of polarity with each other. I don't have to bother worrying about selecting the cabinets - the amps are set to MUTE when bypassed, so they do not continue to feed their cabinet when they are bypassed.
This gives me 4 amps per preset - due to the X and Y axis, and also 4 cabinets. Although, I don't criss-cross the amp outputs so that they can both access both cabinets. If I did that, I would have to have a modifier that mutes the unused cabinets, unless I wanted the amps to feed 2 cabinets at the same time.
That is the great thing about the Fractal. Each player can set his up to suit his special requirements.
Good luck and happy tweaking.