A bit late, but in case you're still looking for this answer, you can have different sounds between each channel but you can have only one instance of an effect in the whole chain, you can't have different settings of the same effect in the two channels (e.g. two Preams in the same patch). There are some effects who have "clones" inside the FX1 and FX2 effects (like Sub Delay, Sub Comp) but there isn't a "Sub Preamp".
If you need to switch a single parameter like the cab you can get crafty with assigns, having one CTL pedal switching to channel A (clean) and setting the cab to 8x10 and the other CTL pedal switching to channel B and setting the cab to 1x15.
However I think it's easier if you just create two patches (one clean and one overdriven) and switch between them while playing

. That way it will also be easier to make sure the volume is the same.