The only sure way to get this working 100% of the time is to use vmware. Wine is fine for some simple programs, but anything that is dealing heavily with copy protection is always going to be problematic.
Vmplayer is available at no cost for all the major distros. You can also create a vmware virtual machines with free tools.
http://www.easyvmx.com/
As long as you have a Win install disk it's a fairly easy procedure to get your virtual Win box up and running. I've been using Quicken like this for years. The only tedious thing with virtual machines is getting your files to and from the host computer, but since the files are going to your ereader directly this won't be an issue.