As Mainstage 2 doesn't have it's own sequencer you can't automate within the application... but I believe there is a way to use Logic simultaneously for timeline automation of Mainstage events. You'd need to connect MS2 and Logic 9 via IAC and perhaps Rewire... I'd have to check this out in more detail...
But the big question is... whether running Logic and Mainstage simultaneously during a Live performance is a good idea...
From your question, I wonder if this wouldn't be easier to achieve using a foot pedal.
e.g. at a certain point in your song you wish the guitar to have a delay... well, you could connect a MIDI controller or foot pedal and have it control the bypass of the delay effect plugin on the guitar channel strip... this would need to be controlled manually... but the beauty of foot pedals are they can be controlled far from the computer and by any band member if you wish.
Hope that helps