That is very cool! A tutorial on how to accomplish this would be very useful for those people like me that are noobs at using any kind of Linux, but would like to run WinUAE instead of EUAE, without having to use Windows of any kind to host WinUAE.
1) Download and extract the winuae archive.
2) Put your kickstart image in the usual subdirectory. If possible, chuck in a working hard drive image or directory.
3) If you don't already have it, install wine. Installation depends on your distro, but I just installed the version from the repository (via apt-get install).
4) Move the WinUAE directory to ~/.wine/drive_c/Program\ Files/
5) CD into said directory and type wine winuae.exe
6) Configure as you would under windows. If you want to point any of the paths at somewhere on your host linux filesystem, it's usually mounted in WINE as drive Z:
7) give it a spin