You could make the BootX box unchecked by default, and when the user tries to check it a warning comes up that says overwriting the BootX file could do damage or whatever and make them click "Yes, I Insist".

Also, when I tried to delete my Aqua backup, I got the eternal progress bar, but after I did force it to quit it seemed like it did delete it. Where does it store the Aqua backup anyway? Another thing about the Aqua backup, it doesn't seem to be backiing up the BootX (very important I'd think) or the menu items that several themes change. Is this right? Can you make it do these in the next version? I love how ThemeChanger is going. It's the only one that's consistantly worked for me. Good job!