BC w/ the Marshall head, labeled "SOUL", and slant cabinet, Marshall logo modified to say "Mars"

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All of the Siamese Dream rhythm sound was done by plugging an EHX Big Muff Pi into the low gain input of a 1984 JCM800 (2203) head set with the master volume all the way, and used the preamp gain to make adjustments. The head was modded for KT-88 power tubes [wiki] because Billy thought they added a very round fat tone to his sound which a huge part of the Siamese Dream sound (he hates EL-34s). It is not recommended to use these tubes in your guitar amps. They are meant for high end audio power amps, and therefore they do not distort easily. They are designed so they stay clean even when the amp is cranked (you don't want powertube distortion in your stereo, right?). Tubes like EL-34s break up and distort nicely at high volumes adding a whole other tonal characteristic to your distortion. Billy bought the amp off "some stoner guy" (included a 4x12) years ago and the cab ended up being used on almost all of Siamese Dream & Mellon Collie, and during the Gish days, it was the only cab Billy used live.
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The following are some clips from a blog post by Kerry Brown in October, 2009:

Mike (Billy's guitar tech): Billy had a Roland Jazz Chorus amp he wanted to find something that would push more air to fill bigger rooms and cut through Jimmy's powerful drum sound. He was looking for a more aggressive sound. So he found an ad for a used JCM 800 and Marshall slant cab in town and asked me to go with him to take a look at it. We went to the sellers apartment where we found an empty room with just the amp, the cabinet and the seller. There wasn't a bit of furniture in the room. It was a bit creepy. As Billy worked out a deal with the seller I took the amp apart and checked it out. It looked great, we tried it out and is was decent sounding. So he cut a deal and we took it home.

To get it ready for the road I wanted to make sure the tubes would hold up and I had no idea how old the current tubes were, so I ordered new ones. We didn't have much money back in the day but I was able to find a good deal on KT88s at Antique Electronic Supply and ordered a set. When they arrived I tossed the old tubes, installed the new ones, biased the amp and I gave it back to Billy. He just loved the way it sounded. In fact over the years as the band had more money to spend on gear we tried "better" more expensive tubes and he always had me go back to the KT88s from china.

Billy: When I first bought the amp in 1989 from this stoner guy, I thought it sounded ok but I think I was more excited to just be playing thru a Marshall. I realized after a time that I wasn't that crazy about the sound so I asked Mike to look at it and see what he could do. After he changed the tubes to the KT88s the amp just sprang to life, and it was the body of the amp that I used to drive insane amounts of distortion into to get 'that sound'. Butch Vig and I were so sold on the sound of the amp that outside of a few select parts, I would say that 98pct of all guitar parts on the first two albums were done thru this amp/speaker combo. In order to change the sound, the Stratocaster parts would be recorded through a shure 57 on the bottom right speaker, and the Les Paul parts would be recorded through a Sennheiser 421 on the top left speaker. This subtle difference between what speaker we would use created the sense of playing thru a different amp set-up even though obviously I wasn't.