Sadly it won't really work well with multiple APC unit in Lightjams, since the APCs doesn't have any settings for which channel and such they send on, so they will most likely use the same channels and same notes, atleast to a large degree.
I've tested quickly with our APC40mk2 and APC mini, and they use the same notes partly. The APC mini only send on Midi channel 1,notes for buttons and CC for the faders, but the APC40mk2 uses 9 or 10 Midi channels for outgoing messages and all 16 for incoming (making it pretty cumbersome in Lightjams). The RGB Pads listen to 1 note each on all channels, reacting differently depending on which channel it receives a note value.
As far as I know the units won't crosstalk by themselves, but if you map something in Lightjams to a specific Note or CC, it will be triggered by both units if both use the same Note or CC (which is likely) same goes for outputting Midi, both units will receive it and react accordingly.
Afaik there is no way to tell Lightjams to send a specific Note/CC on a specific channel to just one unit listening to that channel. You can just select to use or not use Midi in or out from/to a unit.
That tells me that it should technically be possible to do such a separation, but would probably require a large rebuild of the way Lightjams handles Midi.
I would love a different way to handle Midi output, instead of or in addition to patching it like DMX, it could be more integrated to the Midi in (and the way Midi In is handled now is great btw), say that one got an option to return the incoming signal to the same Note/CC on the same channel and unit. And with some options to modify the outgoing signal.
As an example, a source receive a Note with value 127, and I want to send 47 back to the same button, turning it say blue. If I select toggle on the incoming Midi, the outgoing is toggled as well.
If one could also set the value that is sent when not triggered, that would make it very easy to use RGB and other multicolor buttons.
One option for you Francis could be to use something like Bome Midi translator and just have it take signals from one of your APCs and just transmit the same notes/cc on a different channel, and then use the in/out from Bome in Lightjams instead of the signal directly to and from that APC. I've done basically that with Novation Automap for our Launchpad to get it on a different channel than the APC40mk2 to be able to use both. Sadly that doesn't seem to work with feedback to the Launchpad, but I think that's a problem with Automap.
It's sad that AKAI really make it hard to use APCs to their full potential with anything other than Ableton, for their other devices they have mapping software where you can change what is sent and on which channels.
I would recommend that you look at the MPD2 range, they have proper software and they have pressure and velocity sensitive pads and that is just fantastic with things like blinders, strobes and any dynamic lights. I have the MPD218 and use it together with our APC40mk2, looking at getting an MPD226 or MPD234 in the future as well. The MPD218 have 16 pads with 3 banks (so 48 pads) and 6 rotary knobs in 3 banks. Sadly only red light in the pads so can't really color code them, but the bigger models have RGB pads and 4 banks on the pads. Especially with the MPD234 you get a fair bit of extra buttons besides the pads, and 8 faders and 8 knobs in 3 or 4 banks.
So I'd actually recommended the MPD234 rather than the APC40mk2, but they should make a feat pair :)
UA Akai APC20 8xNote@49 (10ch.) MIDI Note C9 1 APC20 UB Akai APC20 8xNote@49 (10ch.) MIDI Note C10 1 APC20 UC Akai APC20 8xNote@49 (10ch.) MIDI Note C11 11 APC20 UD Akai APC20 8xNote@49 (10ch.) MIDI Note C12 21 APC20 UE Akai APC20 8xNote@49 (10ch.) MIDI Note C13 31 APC20 UF Akai APC20 8xNote@49 (10ch.) MIDI Note C14 41 APC20 UG Akai APC20 8xNote@49 (10ch.) MIDI Note C15 51 APC20 UH Akai APC20 8xNote@49 (10ch.) MIDI Note C16 11 APC20 UI Akai APC20 Note@81 (7ch.) MIDI Note C9 11 APC20 YA Generic Dimmer 8 bits (1ch.) MIDI Note C1 43 lpd8 YB Generic Dimmer 8 bits (1ch.) MIDI Note C1 44 lpd8 ZA Akai APC40 8xNote@49 (18ch.) MIDI Note C1 49 APC40-note ZB Akai APC40 8xNote@49 (18ch.) MIDI Note C2 49 APC40-note ZC Akai APC40 8xNote@49 (18ch.) MIDI Note C3 49 APC40-note ZD Akai APC40 8xNote@49 (18ch.) MIDI Note C4 49 APC40-note ZE Akai APC40 8xNote@49 (18ch.) MIDI Note C5 49 APC40-note ZF Akai APC40 8xNote@49 (18ch.) MIDI Note C6 49 APC40-note ZG Akai APC40 8xNote@49 (18ch.) MIDI Note C7 49 APC40-note ZH Akai APC40 8xNote@49 (18ch.) MIDI Note C8 49 APC40-note ZI Akai APC40 Note@81 (11ch.) MIDI Note C1 81 APC40-note ZJ Akai APC40 Note@1083 (8ch.) MIDI Note C9 59 APC40-note ZK Akai APC40 CC@49 (8ch.) MIDI CC C1 49 APC40-cc ZL Akai APC40 9xCC@17 (8ch.) MIDI CC C1 17 APC40-cc ZM Akai APC40 9xCC@17 (8ch.) MIDI CC C2 17 APC40-cc ZN Akai APC40 9xCC@17 (8ch.) MIDI CC C3 17 APC40-cc ZO Akai APC40 9xCC@17 (8ch.) MIDI CC C4 17 APC40-cc ZP Akai APC40 9xCC@17 (8ch.) MIDI CC C5 17 APC40-cc ZQ Akai APC40 9xCC@17 (8ch.) MIDI CC C6 17 APC40-cc ZR Akai APC40 9xCC@17 (8ch.) MIDI CC C7 17 APC40-cc ZS Akai APC40 9xCC@17 (8ch.) MIDI CC C8 17 APC40-cc ZT Akai APC40 9xCC@17 (8ch.) MIDI CC C9 17 APC40-cc ZU Generic Dimmer 8 bits (1ch.) MIDI Note C1 37 lpd8 ZV Generic Dimmer 8 bits (1ch.) MIDI Note C1 38 lpd8 ZW Generic Dimmer 8 bits (1ch.) MIDI Note C1 39 lpd8 ZX Generic Dimmer 8 bits (1ch.) MIDI Note C1 40 lpd8 ZY Generic Dimmer 8 bits (1ch.) MIDI Note C1 41 lpd8 ZZ Generic Dimmer 8 bits (1ch.) MIDI Note C1 42 lpd8