copy/paste your Keyclone folder? Set one up for 5s, and the other up for 2s.

And, how do you command run Keyclone? I, for example use

a;b;c;d;e

it loads all 5 up at the same time which i like. If you dont want to load at the same time maybe just type:

a

load that wow up, dink around with your setting or something and then go KC and command

b;c;d;e

Is this what you mean?