I myself use Outlook 2003 and I noticed I could make an email rule that would sort mail to a folder based on which account received the mail. I briefly tested this and it seemed to work.
I created a rule by going to Tools > Rules and Alerts. Then I chose to create a new rule and to start with an empty rule. I check messages after they are received, via the <name> account (select this option and click the blue hyperlink in the box below 'step 2' to choose the account name) and then I move them to <folder> (select this option and click the blue hyperlink in the box below 'step 2' to choose the folder you wish to move them to). Click Next a few times in between and click Apply. (Note that names may slightly differ as I'm using the Dutch version of Outlook 2003.)
I also found
this page with information, but that method will surely not always work, whereas I think my method should work in those cases as well.
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