Couldn't you just create different "commands" with multiple regions and launch whichever commands you want?

For example I use Main and Alt for Region0 and Region1 (one per screen). You could create multiple regions, set up a command for each one, and only launch the ones you want.

Then when you launch keyclone you'll have the Connect button with the drop down that you can use to launch the game.

Main;Alt
C1;C2;C3;C4;C5
P1;P2;P3

etc etc