This is how my Garcia preset is set up. The name -- M4 S E120 Loop 1 refers to what I used modeling this tone with the "real" equipment ... Egnater M4 with T/D module for the amp, E120 speakers (custom impulse response file taken off my Hard Truckers 2X12 with E120s). Loop 1 is basically the effects loop I describe below; there is also a Loop 2 setting which is identical except for reversing the drive on the envelope filter, for the 76-79 Dancin' in the Streets sound. That's the only time I don't use Loop 1 during a show.
Following the white lines, which represent the digital "cables": The stacked blocks on the lower left represent the effects only, running through the guitar's effects loop. It starts from the bottom left, with a filter block to bring the signal level up louder, to the pitch (octave), wah #1 (q-tron), drive (distortion +), a send then a return that gets it up to the next row and has no effect on tone, phaser (10-stage ala phase 100, rate linked to expression pedal), wah 2 (wah wah pedal linked to expression pedal), delay (tempo linked to tap switch on ground control pro).
The FX Loop block on the right is where either just the straight guitar signal starts, or the signal from the guitar's effects loop hits. In other words, the guitar signal is either "entering" the chain down on the lower left Filter block, or it's starting right at the FX Loop block and never seeing those other blocks, just like the physical effects loop on the Garcia wired guitar. Basically, throwing the toggle on the guitar itself adds in all those effects blocks, and those individual blocks are either active or bypassed by hitting the assigned switches on my Ground Control Pro.
Then we have the amp block, a parametric EQ which is basically a little midrange shaping I came up with A-B'ing the AxeFX setup against my big "real" Jerry rig, then the cabinet block with the E120 IR active, without a microphone simulation turned on. The spring reverb I like to run in parallel, sounds a little crisper and springier that way to me, so it splits off the signal after the parametric EQ block and gets mixed back in with the signal from the cabinet block. That goes out through one last filter block, which is basically a 6 decibel clean flat boost that I like to kick on during my solos.
I own the AxeFX Ultra, which has more memory and a slightly improved reverb algorithm and pitch block algorithms. You can see at the top right that this particular preset is taxing the CPU at 74 percent of its capacity. If you get up in the upper 90s on capacity, you can have some issues.
The amp portion of it is pretty simple. I don't use any power amp simulation, just the basic Fender style preamp controls, a little tweak to the presence frequency and a couple of other things, then the parametric EQ to boost the mids a bit more.
The rest of it is in your fingers!