Swampdonkey:
I feel you. I too am frustrated by the physical layout. But the tones I get more than make up for the lack of flexibility.
I have just modified my approach. The concept of scenes is alien to me. I can see the use, but I dont want to sit here and program out every aspect of what I am doing.
I much prefer the concept of switching on/off effects. I am also using the default layout, so that gives me stomp box control of OD, Delay, and reverb. When you power on, you gotta hit the middle footswitch twice, and then hit effects.
I build my own patches and I do it like this. Marshall amp into a greenback or tv mix cab. Then I put a tube screamer or tone of kings in front of it, usually set for boost. That way, I have a cleanish tone(roll the guitar volume back to really clean up) a lead sound with the OD. I usually then, after the cab, add a reverb and tape delay. I like the tape delay because it adds some modulation.
I really dont use any other effects. I tried tap dancing for the layout stuff to access other effects. Way too hard to remember everything, play and tap in and out of the layouts too access three new effects.
Scenes is too rigid, all or nothing, but I did set one up clean w/ echo, chorus, a nice rhythm sound and a lead.
This video helped me tons, even though it is the AX8, the principals are the same except for the footswitch assignment.
https://www.youtube.com./watch?v=ij53F_NVurY
I cant figure out why they didnt do the FMx in the AX8 format, I'm sure there was a good reason. The FM3 sounds better, but in my opinion takes a step back in practical usability.
I am very happy with the tone I get.