I think you have to distinguish here, are you looking for a good clean sound and not worrying at all about the lead channel? Because when i had my studio pre i found it pretty close to impossible to have a great clean, but have a great crunchy high gain lead channel as well. One sacrifices the other. Best thing you can do would be to dial in your clean first, then work on the lead channel, but you may need a stomp box to get into the really high gain territory. I moved away from the studio for a while bcause of that very reason, couldnt get both a good clean, and a high gain rhythm tone, now i'm shoppin for a studio pre again since i'll be using a different preamp for my cleans.
EDIT - the thing with the the studio pre is really it is 1 channel cascaded into 2. The character and gain of the first channel spills over into the lead channel which is why the gain of channel 1 affects how much gain you will have in channel 2. Its basically just a single channel amp with an extra channel of gain added in.