I'm not using Pro Tools so I don't know the exact settings within that app, but here's how I set up the Axe for use with Logic Pro X.
For recording:
AXE : I/O > Audio > Main Input Source = Analog (In 1)
AXE : I/O > Audio > USB/DIGI Out Source = Input
DAW : dry track input = SPDIF IN
Audio Interface : Clock Source = SPDIF IN (from the Axe)
This will send the guitar input directly to SPDIF OUT. You could also attach your analog Output 1 signal to the interface analog inputs and record/monitor the wet signal.
For re-amping:
AXE : I/O > Audio > Main Input Source > SPDIF/AES
AXE : I/O > Audio > USB/DIGI Out Source = Output 1
DAW : dry track output = SPDIF OUT (unarm record to avoid feedback!)
DAW : re-amp track input = SPDIF IN
Audio Interface : Clock Source = Internal
This will send the SPDIF Input through the patch and have it appear at SPDIF Out as Output 1.
In both cases (initial recording and re-amping) your tracks will have the same input (SPDIF IN). Watch for a loop on the dry track, if it is record-enabled when you re-amp it may feed back on itself.
Hopefully this helps. It is a bit of a pain to change all of these I/O settings. Sure would be nice to have this accessible via Axe-Edit and/or have I/O "scenes":
http://forum.fractalaudio.com/axe-e...modify-input-output-routing-via-axe-edit.html