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If you have separate "accounts" as managed in Apple's System Preferences panel, you should each only have your own email account registered in the Mail application. So check Preference -> Accounts in the Mail Application. If both mail accounts are listed, you should delete the mail account not associated with the main account.
Before you do any deleting of accounts, make sure you do a backup. (Time Machine is a great option.) You may also want to archive any saved mail and possibily import mail from one main account to the other once you have the accounts in the right places.