I'm going to give this one a stab because I think I know what you are going for and I see the complexity in your issue here.
First, let me restate your question so it's more clear what we're going for here. Given some number of pedals with wet/dry outputs, you would like to have a true stereo sound where the wet outputs are sent to your designated "wet" amp, and your dry sound travels through the chain to your main amp. The complexity occurs when you are running two simultaneous stereo effects. How would they mix? How can I control how and when they mix? I think you could solve this problem in one of two ways, both of which are closely related.
Option 1: Use a standard looper and hack it a bit. Take a look at this (poorly drawn) picture:
This one's easy enough to understand and probably the way I'd go. You simply connect all the stereo outs for the pedals you have to a mono looper and turn them on and off based on which effect you want. This would require quite a bit of tap dancing if you swap out sounds a lot, but would buy you the ability to remove specific instances of a pedal from your stereo sound whenever you like. If you use a looper already though you would have to add another one to your board--which could cause space problems.
Option 2: Use a stereo looper. Another powerpoint born masterpiece ahoy:
Stereo loopers allow you to pull the effect entirely out of the chain--both stereo and main lines. This would be useful because if a stereo effect is off, you don't really need it in the chain at all--unless you run into a caveat with true stereo pedals that I'll get to in a bit. If you go this route, you would likely need a stereo looper for your stereo effects and another looper for non-stereo effects which can result in nested loops, and that gets just plain complicated. This might be a good solution if you don't use many stereo pedals or they are localized to a single module on your board (i.e. delay, or modulation, etc).
The caveat I mentioned earlier is related to what some people refer to as a "true" stereo effect. Stereo effects as we know them usually have a wet and dry out, but some of them have true stereo on both left and right channels. This is a bit different, and results in the effected sound coming out both jacks in left and right channels (<rant>which is how it should be, but that's another issue </rant>). In this case, it might be beneficial to be able to entirely remove the stereo pedal from the chain instead of just the effected signal like I described in option 1. Alternatively, you may like the idea of playing the left (or right depending on how you plug it in) stereo channel through your primary amplifier while your wet amplifier receives no effected signal at all. If so, then choose option 1 instead of this.
So in summary there's not really any great solution for what you are trying to do without complex switching strategies. You can always build or purchase your own custom true bypass looper; the folks over at Loop-Master are great for that. I have provided a couple of easy to build or economically sound solutions, but you can always invest in a gigantic rack system that would achieve exactly what you wanted to the greatest degree of pickiness--including a nice programmable floor command center like the pros use.