It would only matter if you are playing the music through a stereo amplifier and expect certain sounds to come out of each specific speaker. Or, if you are recording yourself live over another track, and your guitar is panned to one side, and it is supposed to be grouped with particular instruments which are also panned to that side.
Otherwise, worst thing you can do is flip left and right channels, but they will play just fine. If your stomp is summing L&R to mono, it will sound the same either configuration you plug them in.