The AxeFX is arranged in "blocks" ... each block does one specific thing. Your preset can have an amp block (or two), a cabinet block (or two), overdrive blocks, phaser blocks, reverb blocks, delay blocks, etc. etc. These blocks can be arranged in any order or moved at will. Put your reverb after the amp, or put it before, put the phaser after the speaker cabinet if you want, etc.
The AxeFX also has two independent sets of stereo inputs and outputs, with their own input and output volume controls.
There is also an effects loop block you can insert anywhere in the signal path which will direct your signal from the first set of inputs to the first set of outputs, then let the signal back in with the second set of inputs, within the same given preset.
So, my Garcia preset puts the guitar's OBEL's output into input 1, where it goes into an octave block, envelope filter block, phaser block, overdrive block, wah block and delay block, then it goes into the effects loop block, where it leaves the AxeFX on output 1, and goes back into the guitar. Then the guitar's primary output is plugged into input 2, where it is directed to the amp block, EQ, cabinet block and reverb block, then it leaves the AxeFX via output 2 and goes to the board and to my stage monitors.
When the guitar's OBEL is switched on, my signal starts at the first block (the octave block) and goes through the entire chain. When the OBEL is switched off, my signal starts at the amp block and goes only to the amp, speaker and reverb blocks. Input-output level one controls the volume of the effects blocks, and input-output level 2 controls the volume of the guitar. I set these levels to match.
This offers the same advantage of using the OBEL for "real" effects, i.e., the set of effects blocks are seeing 100 percent output from the guitar's pickups and can be set to the sweet spot, but the guitar's master volume is controlling the output level in the final stage.
These independent inputs and outputs mean, essentially, that you can run four instruments through the AxeFX simultaneously, each with different effects, amps, cabinets, etc., all in one preset, using panning for the blocks ... i.e., guitar is right channel of input one, guitar 2 is left channel of input one, bass is right channel of input 2 and keyboards left channel of input 2. Some people use it for rehearsing an entire band that way.