Hi Dan,
I've had a Helix Floor for a good while.
There's no absolute right/wrong when recording the output of Helix.
If you want to record a Helix signal chain that includes stereo ambience (delay/reverb/modulation), you'll want to record in stereo.
If you're going to do all that type of processing post recording, I'd recommend recording mono.
The switch to turn 48v Fantom-Power on/off is in the Global Settings.
Press the Menu button... and press down on the 6th knob to select Global Settings.
Now... you can use the 2nd knob to turn Fantom-Power on/off.
Helix is a very capable guitar processor.
The more familiar you become with the details, the better results you'll achieve.
If you haven't already, grab the latest firmware update.