You don't download TO an e-mail account. You download FROM an e-mail account with the provider to a WLM database on your PC
I don't have WLM, but in Thunderbird (another e-mailclient) there's an option in the account settings to start a download from that account (or not) when the program starts and to repeat it every x minutes (or not). What options does WLM have?
If your wife and you download to different WLM 'databases' in different Windows accounts (that's not clear from your post), you simply delete your wifes e-mail account from your WLM settings, and your wife deletes your e-mail account from her WLM settings, and everything is totally separated.
I have two email accounts for myself and my wife on a Win 7 laptop. When I start WLM it always downloads to both accounts. Is there a way to run off the auto download and be able to only download to one account when desired?