My (heavily modified) strat has a stereo jack, one side sending the regular magnetic pickups' signal, the other side sending the Fishman undersaddle piezo pickup's signal. I have a stereo jack cord which splits at the Axe-FX end into two regular tip&sleeve mono 1/4 inch jacks. One goes to the front input for the strat pickups, the other goes to rear input 2 for the piezo.
A typical signal routing chain would look like this:
.............[FXL]--[amp1]--... to ouput
--[wah]--[amp2]--[cab]-/
Sorry for the poor Ascii graphics... there is nothing between the left-most "input" and the FXL block, I had to use dots as spacers to line things up. The rear input 2 is fed (through the Effects Loop block) into a clean acoustic-like amp model, then whatever other effects I need. The front input 1 is fed through the grid into a wah, an amp, a cab, and more stuff. I usually then join the two rows for shared blocks (i.e. delay and reverb following a volume block). I use an expression pedal to gradually phase from one signal chain (piezo into clean amp) to the other (magnetic pickups into higher gain amp and cab).
This works perfectly with one exception which had me scratching my head when I first set it up. My FRFR monitors are plugged into Output 2 (I use Output 1 balanced out to my computer's audio interface when at home or to FOH when at a gig). When I first added that Effects Loop block, however, it cut off my signal to Output 2 (I use "copy out1 to out2" in the I/O menu). You see, the copy out1 to out2 works only when no Effects Loop block is used (the Ultra manual says "If the effects loop block is in the grid then this setting is ignored"). So it's just one thing to keep in mind when you set it up.
Other than that, it works beautifully. My example is for a single patch that allows you to fade from piezo to magnetic into different signal chains, but if you set it up as distinct patches, it will also work. You will need to have your Effects Loop block in any position except the first column (if you put in in the first column, a connection is automatically made between input1 and that block). When you switch to that patch, no signal will come from input 1, and your effects loop block will route your piezo signal from rear input 2 to whatever else you put in that chain.
