By default, all email from all accounts goes into the same Inbox.
There are four different ways of changing that:
1. Use separate Windows user logins. That gives total privacy, and is
ideal when two different people use the same computer.
2. Use message rules to filter incoming messages into
separate mail folders.
3. Upgrade to Windows Live Mail which has separate folders for each
account, no rules needed:
http://download.live.com/wlmail
4. Purchase an add-on called WMIDs:
http://www.oehelp.com/WMIDs