SP were my favorite band growing up when I was learning guitar, so I've spent a lot of time researching for and building patches for Siamese Dream and Mellon Collie sounds (I use FM3, fair warning). A few things I've noted (and I'd be happy to share the patches if someone wants to check them out, I just haven't done that before so I'll have to learn how).
Siamese:
I use the JCM 800 model and alter the tube type to KT-88, turn master volume to full, and use gain control as master volume. You have to keep it very low to keep the amp clean for clean parts (all of the distortion will come from the big muff). I tried to pick cabs similar to the vintage 4x12 Marshall ones Billy used but you can use your ears on the IRs. It can help to use a compressor before the amp to make sure the clean tone stays clean, depends on the guitar. I can't recall exact b/m/t settings but that's sort of to-taste.
For the distorted tone, put the PI Fuzz in the chain and swap out the transisters to OpAmp type. Set the volume and sustain to full, and then use the tone knob to search for the SD fuzz frequencies. I find that for my guitars, it's somewhere between 1:00 and 4:00, but it varies by guitar. This whole approach is more or less taken straight from interviews.
For solos, like Cherub Rock, I use the zero-through flanger with an extra 2-3 db of gain, and I can't tell you anything about my settings without looking, I experimented until it sounded right. On the record they use actual tape flange so no particular pedal is going to do that exactly.
Mellon Collie:
Focusing here on getting the distorted sound (a la WBFTT or Jellybelly). Billy's original rig is a Marshall JMP-1 with dual Mesa Strategy 500 power amps in stereo. The best I could do to replicate this was to use the Brit Pre (can't remember the name of the channel, it's OD2 bass response or something) and then make all the power amp settings as similar to the USA Pre power amp settings as I could. Maybe this is a naive approach but it sounded good so I went ahead with it.
Similar to the SD set up, Billy sets the amp at max volume and uses the gain control as a volume, so for clean sound you need the gain very low. In the live setting he was using an Alesis compressor in between the pre-amp and power amp to drive additional volume and slam the hell out of the power amp. The approach is trying to get as much of the drive as possible from the power amp. I set the pre-amp master volume at max, and the gain control at about 9:00 or less for clean sounds, but for distortion, at least noon or more on the gain, and then also engage the boost circuit, probably to max. It gets that muscular Mellon Collie distorted sound, and it's the only way I could think of to do the boosting between the pre-amp and power amp sections, without getting too much of the pre-amp distortion sound.
Similar on the cabinets as above, I experimented with combinations of the 60's marshall 4x12 cabs until it sounded good to me. There's a lot of bass in the mix which I get from the basic amp controls. It's a bit out of control, it will spit noise at you if you're not playing, but that's how his guitar sounded live on that tour so I look at it as goal achieved.
If I get the Axe III (always considering it, just need to save up) I think I'll try doing a stereo rig with dual amps, so I can use the Tri-Axis on one channel to represent James, and the JMP-1 in the other for the Billy sound, and see if they blend into a better approximation of the album sound.
Bonus Points: Gish
Since there's no ADA MP-1 model in the Fractal, I just found that if I use the Friedman HBE V3 with my Strat it sounds very good and I don't really miss any additional verisimilitude.
. the mix is bad to me . Some records don’t go better with the time 
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. That’s the secret !!!! Joking . Don’t know
It has always been a huge favourite of mine.