I have used two layers of microfleece for a T&T diaper cover before, and it worked just as well as a 1-layer cover of "regular" (200wt) fleece. I've also done 2-layer covers of 200wt. fleece outer with microfleece inner. I actually like them better than 2 layers of 200wt, because they are trimmer without losing too much protection.
Technically, *all* fleece wicks. Fleece works by dispersion--it spreads moisture out over a large surface area (without feeling wet to the touch) so that it can evaporate. Because microfleece is thinner, it wicks faster (there isn't as much there to spread the moisture out in), and putting something absorbent "behind" it causes the moisture to be pulled into that absorbent thing instead of sitting in the microfleece--which is why pee goes through the microfleece in your pocket diapers. Thicker fleeces don't work as a "stay-dry, wicking inner" because the fleece is too dense to wick *fast* enough to stop the moisture from just puddling up and leaking out.
The only way your plan would be a problem is if you put something absorbent in between the Windpro outer layer and the microfleece inner layer (but then you would have an AIO and not a cover

). But wicking is actually what you want (to some degree) with a fleece cover, and Windpro is more water resistant than "regular" fleece, so you shouldn't have any problems

HTH!