So you're gonna want to put the El Capistan in the FX Loop of the AxeFX instead of in front of it. This might be obvious, but it's for multiple reasons. Not only do you not have to stomp on it to turn it off or on, but you're able to put it either in front or after the amp and cab block based on each individual patch. So from the FX Loop Out of the AxeFX, connect it to the Input of the El Capistan. Then from the Output of the El Capistan, connect it to the FX Loop In of the AxeFX. Whenever you have an FX Loop block set in the signal path now, it will run it through the El Capistan. Then adjust the Output 2 and Input 2 accordingly so you're not clipping the input.
That's the basics on how to set it up. This is where you can get more advanced with customization of the chain. Some people run it in what we call "series", which means that it's one straight signal chain. It would go (in a basic setup) amp->cab->delay->end of signal chain. Simple enough. BUT if you want the dry signal to be kept more intact (not to be run through the converters that change it from digital to analog and back when you're sending something to the FX Loop), you can run it in what we call "parallel", which means that right before the FX Loop block, you split the signal into two signals: one of them goes straight to the end of the signal chain while the other branches off, runs through the FX Loop and then rejoins the original signal. If you were to do this, turn the mix on the El Capistan pedal all the way to 100% as you don't need it to have any dry signal running through it. That way, instead of a "mix" control, you just adjust the "level" control on the FX Loop block Sorry I don't have access to a picture that I can show you of this. I'm sure someone might jump in if you want more info on it.
Another fun part about using a physical delay in the FX Loop is that you can set spillovers from it VERY easily. Spillovers using the delay blocks are not the easiest to set, but all you have to do with a physical delay pedal is to set an FX Loop block with nothing running into the input but have the output of it connected straight to the end of the signal chain. This separate signal chain will run along side your normal chain for that preset. I might even suggest setting something like this up on most patches that don't use the El Capistan so it can have trails. Especially if you normally set the El Capistan as the last effect in your patches.
I know some of this may be a little more advanced than you're looking for, I just get excited about all the stuff you can do with physical delay pedals in the FX Loop!
