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I'm far from an expert on Catobase, but as a longtime user here are a couple of answers:
You should run Catobase once per season, when you finish that season. Those of us who've grown accustomed to using it just back up all the files at the end of each season as a matter of course, since you need to export at that point in order to get all the stuff into the webpages.
I use it solely for my solo league, and just have the "web pages" on my hard drive.
And I think Cato has embedded CommishJoe's exporter in the program now, so there's no longer any need to use the exporter separately (I haven't used 6.0 yet, so someone correct me if I'm wrong).
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