My DAW shows the inputs automatically. In I/O settings I have 4 channels, 1 and 2 is the "wet/Amped" Signal and 3 and 4 is the "dry/DI" signal.
you should just edit your I/O settings in your DAW and that should be it. Then have two tracks in either mono or stereo and record the DI signal as well as the wet/amped signal.
An even easier method for the studio that would not involve modifying your presets would be to go to the I/O page on your Axe-Fx II and set "USB/Digi Out Source" to "Input".