I am also looking at doing something similar to this except without having Windows at all. I am going to load a copy of Dos on one of my old PC's and boot up dosuae as if it were just like the main OS. I posted on another thread about a Dos version of Winuae and done a google search and found the Dosuae page. You may also want to look at this method so you dont have to have Windows on the computer at all. Remember the old days when you had to have Dos to run Windows? This would really be the same thing, just Dosuae replacing Windows and Dos would still be in the background like Windows 3.1 was back in the old days.
http://uae.is.free.fr/