Pegasus made me do that, and it took me years to get the filters and rules set up to the point where I didn't send replies to mail sent to my Student And Business account from my "Hello, I'm A Dragon And A Furry!" account.
Even after I got that working smoothly, it was impossible to generate rules that would consistently work with mailing lists and blind cc:s.
Thunderbird is the only current mail client I know of that gives you the option to treat each individual account as an individual account, with separate inboxes, draft folders, trash files, and whatever, without any magical jigger-pokery. Unfortunately, Thunderbird showed more evidence of the Mozilla Memory Leak than Firefox did on my Windows machine, and Ubuntu is already glitchy-twitchy. If I can't find anything else than handles email properly, I'll go ahead and use it -- but that still leaves the question of why most clients don't.
If there's some hidden trick to making Evolution (the OpenOffice mail client that's the default for Ubuntu) handle mail nonstupidly, please let me know.
If your answer is "Oh, it's simple, all you have to do is set up a few filters and folders and rules", then you fail at reading comprehension. Please return to grade school for a refresher course.