You can use Audacity (free) for capture if you like.
My way:
I use a 20sec 48k/32-bit Float log Sine Sweep. I load that onto its own mono track in Cubase (6.5 currently) in a 32bF/48k session. I set up four more mono audio tracks; one to test mic placement (input is from the mic), one to capture a DI (amp block ONLY) from the Axe, one to capture that exact same Axe patch through a neutral power amp + cab/speaker(s) being captured, and a final one for the Sweep capture. In addition to the sweep, I have an inverse of it, which is what I use for the deconvolution step.
With that session as a template, I can open Cubase and load it up easily, save as a new IR capture run, and go to work. I keep notes in the session regarding mic placement, etc. Cubase also allows me to record to the same track with each pass being a new take (and numbered to reflect this). Other DAWquencers offer this; I like Cubase and Pro Tools. With each track labelled to reflect the source.. such as, "Mic Test," "Axe DI," "Axe Cab," "Sweep Cap"... and with my notes, I can easily return later and know what I did. I will then come up with a patch, get the volume where I want, and start with mic placement. I enable the "Mic Test" track, and start recording and playing back, searching for a good placement; in my current situation, this is easier than having someone play while someone moves the mic until I hear a placement that sounds good to me. When I find a placement that sounds good "on tape," I will record a take on the "Axe DI" and "Axe Cab" tracks. This allows me to return with the resulting IR later, load it into an IR plugin, and compare the DI + IR track to the appropriate Cab + Mic track; IME, if done properly, these two will match very, very closely, almost indistinguishably.
Mic placement set, I make notes, repatch (I use my patch bay) an out from my ADC/DAC I/O box to the input of the same neutral power amp at the same level setting, mic still in the exact same place.. I then solo the Sweep track, and record a pass to the "Sweep Cap" track that exceeds the 20sec sweep length by a small amount. By following this recipe, I now have Axe DI, Axe Cab, and Sweep Cap take numbers that correspond to one another!
Next, I take my Sweep Cap takes, process them in Octave (using the Inverse Sweep I mentioned previously), and then either use the resultant trimmed (based upon the inverse sweep length) files, or use Audacity to trim them manually where I would like. Then I take those files and use Axe-O-Matic to convert them for use in the Axe-Fx II. With Axe Edit, I can then name, transfer, etc. Works great as an editor/librarian for me! Personally, I prefer to limit my IR use to plugins rather than the Axe; please note, though, that I no longer use the Axe for any amp (or front end) duties. For someone opting for Amp Block use, perhaps with an FRFR system, or DI recording, etc, the Cab Block plus your own IRs can be fantastic, and the extra Axe features afforded can be a plus IMO.
Since Octave is a pretty "deep" app, I would also suggest Voxengo's Deconvolver. Oddly enough, I had problems processing captures using sweeps NOT generated by Deconvolver. Unless one desires "deeper" options and versatility, I think that Deconvolver should be just fine. I would suggest using a sweep generated by Deconvolver for your first tries. Maybe someone else got non-Deconvolver sweeps to work with it?
