Certain skins work well between the two different softwares. But that is the problem, you are working with two different softwares. It comes down to the image design. If you design the images so that they will work with both docks, then you shouldn't have to do to much with the configuration files. Practice make perfect in this case but you won't always be able to do them both without having to do some tweaking between them.
Something I've thought about starting is to include rocketdock versions in all my docks, so that both can be used depending on what dock the person uses.
