The basic question is do I only need to run sa-learn from my personal account or from root or both for later system usage.
You need to run it as the same user that spamassassin gets run as when mail comes in. In some setups, this winds up being your account, in most MTA sitewide setups, it winds up being root for everyone.
It sounds like you're calling SA as a result of using fetchmail under your account. If that's the case, then you need to sa-learn from your account.
If you're really not sure, try adding a slightly different spam threshold to your user prefs (like 5.1 instead of the default 5).. then look at the headers of your mail.. if the change took, then that's the user that SA runs as when you get mail.
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