If you use the output signal from either of the devices you plan to use later (your amp, the Floor Pod) I don't think you will have any problem. The output signal from these devices will be much stronger than the dry, unprocessed signal from the guitar itself. Unless you have a specific reason for recording the dry signal I would proceed to your 'later' setup now. Any settings you make with teh Backtrack device now, in order to capture the weak signal, will have to be undone later when you want to capture the processed signal from your other devices. The Backtrack setting for the dry guiitar signal will not work well with the stronger signal.