In that case, you desperately need an external soundcard. Integrated soundcards (as in, on the motherboard like in a laptop) are useless for recording. Extremely useless. Your microphone also has a 6.3/3.5 connector? Those mics won't do if you want a quality recording. For your situation I recommend getting a good soundcard and line the electric guitar, and then reamp is with software, like Amplitube and Guitar Rig 4 - Those softwares are fantastic. Especially Amplitube. That way you won't get any flutter echo, reverb, interference or anything.
Cones on the ceiling sounds good to me.
And by recording stereo, you mean you mic it with two microphones, right? You can get an overall stereo sound by panning several mono tracks, (I do that at home) but stereo
recording is when you record with two or more microphones. Mono vs Stereo depends on the situation - "Gothenburg Metal" bands record stereo with two SM57's, one placed slightly more away from the amp. That's the contemporary technique. Or pretty much, not sure about the mic placement.
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Anyways, Stereo
micing in a room such as yours with your current equipment and situation seems a bit overkill to me. But to use several mono tracks to create a stereo effect is what I think you should do (or maybe that's what you're doing?).
To conclude though, I'm positive the best way for you to record a distorted guitar is through amp modelling, where you line the guitar to an external soundcard (the external soundcard thing is of extreme importance. As I said, the built in soundcard is useless for recording) and add the amp later digitally. Satriani lined his marshall heads and used modelled cabinets on his Professor Satchifunk... album.
Here's a vid of guitar rig and Amplitube.
http://www.youtube.com/watch?v=Xf2CbUAi83U