1) Changing patches from the midi unit, and
2) Switching on/off individual stomp boxes within each patch.
Item 1 I can to, item 2 I cannot figure out.
According to the manual, MIDIMate can work in 3 modes:
Bank lets you acces Program Change messages quickly (to change MainStage Patches)
(You say you have this working?)
The 3rd Mode is "Controller" mode, which you will need to use. It lets you use the bottom row of switches to change Patches as above, the top row (5-9) to transmit MIDI CC messages (which you will need fo rthe stompbox switches in MS).
a) Select "Controller Mode" on the 'Mate, and use Mainstage's Activity monitor to make sure that the Mate is sending CC messages when you work the right pedals. (You should see something like 1 16 127 first number is MIDI channel, second CC number 3rd value 0 for off 127 for ON).
b) Starting with one of the Guitar Templates, go to Layour mode, select one of the switch controls and click Assign (means "Learn") , then press the 'Mate switch 3 times
Rinse and repeat