Assume pre-sales question so ask Sequential/Focusrite directly for cofirmation on what I write.
Layer A and B can be handled like two different synths, sequencer, arp, effects too.
- you have 4 audio outputs to separate two stereo outs
- in global settings set Multi Mode to on, so will be handled like two part synth. basechannel +1 on second part.
Then there are setting for Midi Arp/Seq meaning sequender arpeggiator send their midi data too, not only playing locally.
- but unclear if this data sent on two different channels for each layer or not, ask support
- it is a global setting, not for each layer
So on that detail, channels on midi out, determine Yes/no to your question.