You'd have to ask Satanika if you want a precise answer about the exact nature of the upmix, since he was the one who actually did that. In the past I tried numerous upmixing schemes, all of which refused to work properly on my computer. (I love my Mac, but when software you want is only available for Windows it can be a bit problematic, I have to admit.) I believe he used a Foobar2000 plugin called ATSurround; while not actually a Dolby product, the sonic results are very similar to what can be heard with Prologic II. Actually, ATSurround almost worked for me; it installed and ran perfectly, but while my sound card is capable of multichannel audio, my limited WINE setup will only output 2-channel sound, so I could only record the front left and right channels, and the sound card wasn't receiving the others at all. Because of that, I needed some help getting the thing into 5.1 format, so Satanika very kindly performed that part, and then substituted the LFE channel to replace the one generated by the program.
Since the 5.1 already has built in a rendition of the sound very close to what will be heard from upmixing at the receiver, with the significant added benefit of the LFE channel, I recommend that version be used if the proper playback equipment is available. The stereo version will give better results if surround speakers and/or a subwoofer are not present in the system, since it contains no phase changes or time delays. Such things could compromise the sound of the 5.1 if it were to be downmixed (though I suppose it's down to the individual listener how much a problem that would be).
I ran into a setback on the music edits for Empire, which is that the '93 and '97 mixes don't blend together as well as I thought they would. It took me a while to notice, because on the surface they sound pretty similar a lot of the time, but the levels of background sounds are actually not the same at all, and this disparity made the transitions between sources very audible and jarring. Clearly I picked the wrong switching points, so I have to go back and redo them. Hearing the two versions back to back so many times I'm starting to get confused about which really sounds better for the film, and then questioning whether I should even be doing this at all. Ugh. Had to take some time away from it to clear my head. Oh well, that means more time to work on my writing, lol. I'll try to have it finished as soon as possible. I know I keep saying that, sorry! :)
There actually is a 5.1 version of Empire already that does not contain the music edits--it can be found on dark_jedi's earlier encodes. Aside from the edits, most of the new one will sound exactly the same. There isn't one like that for Jedi--it wouldn't be hard to make one, but since it's not actually me that does the upmixes, I can't provide it directly.