I'd suggest not replacing the shell, just run it as a startup item with a customised WinUAE config. This way, you still have Explorer if you need to exit WinUAE (for upgrades, file operations, etc.)
Once you're in WinUAE there are a couple of packages that allow some interoperability with Windows (running executables, etc.) I've never tried them myself, as I don't run WinUAE a lot.
