My guitar is using Input 2 instead of Input 1 and I'm having trouble using

For Sunday Guitar, since you are processing an audio signal coming from the guitar you have to select that input in MainStage. Some audio interfaces like the Focusrite models have combo inputs that you can plug an XLR or a 1/4” guitar cable into. Other interfaces will have one XLR mic input and then one 1/4” input jack. If your guitar is using Input 2 in your interface, you'll want to select that on the channel strips in Sunday Guitar because by default they are set to Input 1.