In the Midi Control center, you can save preset for the BSP
The modifications you set in the tab Project, Seq1, Seq1, Drum and controller map are local (only apply for one part of the BSP).
You can have multiple configuration and save it / load it when you need to, to do so on the left panel under "project browser" you can save it, delete it, or make new one.
To apply those modifications to your BSP you need to send them to it, to do so on the left panel under "Device projects" you can "Store to", or "Recall from" It's only after clicking store to that the modification will apply to the BSP.
The modifications you set int the Devices settings are global (apply for all the BSP) and MCC save it by itself and apply instantly when you change something. To change the midi channels of any of the 3 Seq of the BSP you doing it here
airutraairutraairutraairutraairutraairutraairutraairutraairutraairutraairutra yep, i feel your pain x)