This wiki article is more layman than the wiki on impulse responses:
Convolution reverb - Wikipedia, the free encyclopedia
Also check out the help for the Voxengo deconvolver.
Voxengo Deconvolver Help
IIRC, the process would be, to run a test signal through the system to be captured. Then record the output.
E.g. for a speaker cabinet capture run a test sweep signal through an amplifier -> speaker -> mic -> preamp -> recorder.
Then the original test signal and the output, the recorded impulse response of the system being captured, are deconvolved.
The output of the deconvolver can be loaded into software, like the Axe Fx II. Then any signal, your Axe patch, can be run back through the convolution. This applies the original impulse response onto your signal, aka your guitar patch.
From what I gather, in firmware 3.0, the Axe II will output a test signal, a sweep. Then by hooking up a microphone to one of the Axe II's inputs, the Axe II will record the impulse response of whatever you are capturing, e.g. you stick a mic in front of your guitar cab and run the Axe sweep through that and back into the Axe.
Then the Axe II will deconvolve those two signals to produce the "IR" data that can be loaded into a patch.
This capture process is like a utility. It's not something you do when you are playing a gig. It is a utility to generate data that is loaded into a patch.
Richard