To footswitch modes on the V-Twin rack pre, you need a MIDI controller pedal and something like a MIDI Octopus (or a MIDI Matrix), and a bunch of patch cables, one for each switch you want to control. The Octopus has eight quarter-inch jacks on the back, and you connect those to the quarter-inch switching jacks you want to control via MIDI. So, #1 could select the Rhythm1, #2 Rhythm2, etc.
On the Octopus, you select the MIDI program that you want to edit, for example 001. Then on the front panel of the Octopus you select all the switches you want to have "on" for that program setting (there's a button for each one). Typically this would be one of the channel/modes and then the effects loop on or off. The V-Twin Rack Pro also allows you to run both the Rhythm and Lead channels at the same time, so you could have three switches in use for a given patch.
Once you've made all your choices, you press "Save" and the Octopus stores all those switch settings in that MIDI Program. You'll probably also have a rackmounted effects unit you're using, so you'll have MIDI cable connecting the effects unit and the Octopus, so you can store all your preamp settings and your effects settings and call up all of them with one MIDI Progam Change command (i.e. a button on your MIDI foot controller).
I used to have a setup with the V-Twin, an Intellifex the Octopus and a 20/20. My MIDI controller was connected directly to the Intellifex, and then the MIDI Thru went from the Intellifex to the Octopus. The Intellifex supports MIDI "mapping", so you can have incoming MIDI Program Changes trigger a program other than the MIDI Program Change number. This way you don't need to have a bunch of copies of commonly used effects patches.