In both FM3 units you'd want duplicate presets from the other unit just in case one dies and you need to switch to the other, or swap them around to even out the wear and tear.
To expand on my above comment...
Caveat: I don't have two FM3 or any MIDI cables here, but this seems like it should work, or at least get you into the ballpark.
See page 113+ in the FM3 Owner's Manual for setting up sending MIDI PC and using the Scene MIDI block, and page 84 in the Fractal Audio Blocks Guide for more specific Scene MIDI block information. FM3-Edit doesn't let you access the MIDI settings, you'll have to do that on the unit itself. Then you can use FM3-Edit to create the blocks and fill in the data.
Assuming you want a one-to-one correspondence of the presets on the two devices:
- Designate one FM3 as the master, and the other as the slave.
- On the master, define your primary/main presets, organizing them into a bank, say in slots 0-9.
- Turn on sending PC messages to make it act as the master.
- On the slave, define your secondary presets for your secondary sounds, organizing them into a bank in blocks 0-9.
- Turn off sending PC messages to make it act as the slave.
- Connect the two units, from the master's MIDI out to the slave's MIDI in.
Test to see that changing presets and scenes work as you want. A PC (program change) message will be sent when changing presets on the master via MIDI to the slave, and the slave should immediately jump to the corresponding preset. If you have the Scene MIDI block set up in presets on the master it should let you toggle scenes on the slave by sending the appropriate CC to switch to the corresponding scene. It doesn't have to be the corresponding scene of course, but for consistency and ease of debugging and to save wear and tear on your mind it'd probably be better to begin that way.
Once they work as expected:
- Copy the bank from the master to the slave, but in a different range, something like 20-29.
- Copy the bank from the slave to the master, using the same bank range, 20-29.
If you need to swap the two units, just switch to the master block on it:
- On the previous slave go to the first preset in the 20-29 range, which are the dry presets copied from the old master.
- Turn on send PC on that unit, causing it to become the master.
- Move the MIDI cable to its MIDI out port.
- Turn off send PC on the other unit, causing it to become the slave.
- Move the MIDI cable to its MIDI in port.
To use the slave to replace the master in case it fails, do #1 above.
You'll have to keep track of which machine is which, so you know which bank of presets to use as primary/secondary. I'd put something visible on the master, like wrapping a nylon wire tie around the guard rail but YMMV. Naming the first preset in the two banks something significant might help make it obvious when looking at the preset list.
Personally, I think it'd be a lot easier to buy an FX3 and a FC-6 or FC-12, because it's at least as powerful as two FM3 and has four OUT blocks so you could wire it up the same way. The added work configuring two FM3 would be wearying to me.