If I were you for monitoring I'd go to Setup in the top right of AxeEdit and go to the Audio Tab on the left column. On the far right of that page set Output 2 to Copy Output 1 On.
You'll give FOH output 1.
If you want to send FOH a consistent level from gig to gig - on the device itself you can go to Setup -> Utilities -> and page over to ADC Levels. I set my Output 1 to 75% (you will see the numbers jumping around a bit and that's normal)
You'll use Output 2 to connect to your monitor. That is the only volume you'll touch all night. Leave Output 1 unless FOH requests a level change.
I have a few presets, but one is a kitchen sink preset that covers most things. I have some crazy stuff for harmony songs, organ sounds etc that are different presets.
As far as FC - I would like to eventually get scenes set up for all songs as that would be easiest.
But right now I have Layout 1 Presets automatically use a layout link to go to the Scenes layout.
Scenes Layout has all 7 scenes and 2 drives and 2 control switches.
I have layout 3 controlling Amp channels and the pitch block channels
Layout 4 is all my gain - all 8 channels of drive plus 2 control switches
Layout 5 is modulation - Trem, Pan, Vibrato, JetFlanger, Enhancer, Filter (solo boost), PredirtFlanger, Univibe, Chorus, Phaser, PostDirtFlanger, Rotary
Layout 6 is Time effects Spring, Ambient, Swell, Plex1, Enhancer, Filter (solo boost), Slap, Digital, MemoryMan, 2290, MultDly1, and Plate
7 is Per Preset, 8 is looper
9 has all the layouts plus a link to my Solo preset if I'm in a pinch to get out of what I'm doing to do a solo
You can really do anything you'd like with the FC12!