Have one for NEW install and one for UPGRADE if this is so confusing for so many users I'd think that would maybe cut down on the amount of upgrade issues.
We used to do this, but keep in mind two packages need to be maintained, which can get quite nasty if something "accidently" gets removed...
There are upgrade doc's in on the site and in the faq forum, it shouldn't be too hard to follow one of the methods displayed...