I have been using MSOutlook 2007 for several months and had two email accounts I had been using that were forwarded via a business website I have hosted with domain.com. All had been working fine.
I just started a job and they had me load MSExchange email for Outlook...I foillowed the instructions and now when I open Outlook on my laptop, it prompts me for the exchange login and I can access my new account. The old accounts are not available. I've tried not logging in to the excahge email, but still no old accounts.
You can set it up to where email FROM different email accounts or from different senders go to certain folders.
I suggest that you make a folder for your seperate emails, or you could get accustomed to looking up top quickly to see where it was sent to.
I personally have multiple accounts going into mine, and just set up folders for people who email me. A folder for friends and subfolder for each one, and they are delivered to their seperate folders with notifications next to them when there is a new message in it.
I pretty much don't care who sends what where personally and am more concerned with checking certain sender's emails more frequently, but your situation probably differs.