I am running a Voodoo GCX Switcher and a Ground Control Pro in a rack. I placed the M13 on a sliding shelf within the rack. If you have the GCX and GCP for your switching system, I recommend the following:
Go into a preset on the GCP (preset 1), set all of the effects blocks on the M13 to taste, go back to the GCP and save the preset (this will save on your Line 6 automatically). Now, you can leave the preset and return to the preset and you will notice that your M13 returns to your desired settings.
Carry on this process for Preset 2, 3, 4 on the GCP. Now, in your song, you can begin the song on preset 1. For the chorus part of the song, you can select preset 2, Solo-preset 3 etc... This is the manner that I use my setup. I like it because I can also name the presets and see the screen on the GCP respond to the selected preset. For the next song, scroll to the next bank and repeat this process. Now you can have your set programmed with the name of each song, chorus, solos etc... right on the screen of the GCP in front of you as you are playing and in the desired order:)