As I become more aware of issues surrounding the use of Fantastico installer, I'm wondering how to plan ahead in the event of upgrade problems. Drupal 5.3 just rolled out and for IntegrativeDesign.net I installed the most recent version. Drupal 6 promises to have a lot of security enhancements and core functionality additions - so we will want to be ready to upgrade our drupal sites when that release becomes available to us. At issue is Fantastico's installation/config changes to core Drupal install that can cause problems for upgrades. This will require some testing and due diligence. In the meantime, I came across the following post in a drupal forum that seems like a reasonable strategy if fantastico causes problems:

"If you have a site installed with Fantastico, it's often easiest to back it up, tell Fantastico to delete it entirely, and install the newest version of Drupal manually. Then import the backed up DB and do things yourself. It's just a LOT safer."