well after reading Ultimate Six, apparently they keep all genetically altered people in one part and evil mutants in another. It wasnt safe however since when Doc Oc escaped he let Kraven, Electro, Sandman and Osborne out with him
Magneto and the Hulk are secluded from the others, it seems like.
Also, the Lizard and SHIELD should continue having nothing to do with eachother. The more characters that fly under SHIELD's radar the better. That's why I was a little upset when Fury came and picked up Sinister. I thought that the police would come and get him. That would be their mistake.
Actually in Ultimate Six we saw that the genetically altered criminals were kept in an entirely seperate facility from the Triskelion. Magneto and the Hulk are the only ones who we know were being kept in the Triskelion itself, and that's mandated by Magneto's high profile and the absolute secrecy around Banner. I don't think there's any other criminals being housed there. Since few of the sorts of criminals SHEILD takes care of would ever be tried publicly or are even known to the public (before Electro's escape it's pretty sure that no one had any idea he existed, Sandman would be more like an urban legend as teh cameras were gone by the time he was set free leaving only a few dozen witnesses who would most likely be called liars or nuts and no one in the public knows about the connection between Osborne and rumours about a goblin monster - only Octavius is generally known by the public), it's most likely that they like the Six are kept in scattered secret facilities.
Yeah thats right. Fury picked him up, and took him back to the Triskelion. Since it also serves as a detention center, they are keeping him there. He's not a super-villain, so I doubt that they'll worry about moving him somewhere else.