Apply color correction to all footage by changing one color?

Hello everybody,
I have two versions of the same footage which I want to synchronize and make one video out of them. By masking, I've put one on top of the other and I'm synching the footage, but the colors are slightly different in the bottom one (a bit brighter). I've tried to correct it using several filters, but even though I get some really good results changing the values (I'm using Brightness and Contrast right now, but I've also tried Color Correction, HLS, Hue/Saturation...) they're not as good as I'd like.
In several moments, for example, the sky appears, in both layers at the same time. Is there any way I can make the bottom layer correct the sky color into exactly the one in the top layer, so the changes I make in the HLS of that color apply to all footage? That way the color changes would be perfect.
Maybe this is easy to do, but I'm a beginner at After Effects so I don't really know how to do it. Online tutorials don't seem to help much either.
Thanks!

I've been using the re:Match plug-in for similar tasks with success. It costs $90 but there is a demo version you can try out:
http://www.revisionfx.com/products/rematch/
and also a tutorial from Andrew Devin:
http://library.creativecow.net/devis_andrew/AE_RE-Match/1
You can also match footage in Speedgrade, but I haven't tried that feature yet.

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Apply color correction to all footage by changing one color?

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