I to would love the gba one. As for whats installed first...I'm not sure how i did it...:-/ If you really want to make sure nothing steals anything from the other, I would install the nintendo one with the regular one uninstalled, save the files you need, then uninstall the nintendo one, reinstall the regular one, and then transfer files...that my work better.
On a side note, i have had them disappear from the list in desktop properties a couple times. I have no idea why this happens, but a simple solution I found it to take all the them folders out of the windowblinds directory, restart windowblinds (now nothing will be available in the desktop properties screen) then re copy the files and restart windowblinds again. That seems to work for me. Like i said, its very buggy and weird how it works, but I have mine working and I only had to do the re-copy think like twice so far.