Hmm...I know it works flawlessly on WinUAE and Amithlon. Of course, both of those are using RTG, so...I would think that you would just have to click on the button, save the settings and reboot.
I do remember having some grief with the 2.21 version, in that it would consistently add the prefs to the WBStartup drawer. After I updated to version 'blah blah (ie, the current version I'm using), it stopped that. If you'd like, Mate, I'll throw the version I'm using on my space and provide a link for you. Don't know if that will help, but it's worth a shot.
Cheers!