This may be of some help. Recently, there have been a few postings on
multiple-association apps, which allow you to associate more than one
app to an extension, which when you click on the file, you'll get some
sort of popup that asks which app you want to open it with. Search
a.c.freeware at groups.google.com for specifics.
Two that have been mentioned are WAssociate and OpenExpert. However, if
you're not sure how to use/install, then just go with the advice
already given.
And, no, deleting the association link will not delete your CUE files.
BTW -- since CUE/BIN files are almost always associated with the same
apps [they typically go as pairs] if you want, you could always
associate the CUE with one app and the BIN with another. Though if
unsure, probably best to leave with the app you most want them to open
with.
Finally, the CUE is simply a little file telling your apps about the
BIN file. If you ever lose or accidentally delete, or simply don't have
the CUE, you can recreate it with a freeware app such as CUEator:
http://www.site.uottawa.ca/~glabr047/cueator.html