If you want two entirely different sets of in boxes, trash folders, etc....I think you'd have to install two copies of the program.
My wife & I have done this with Eudora, and I have 2 'identities' for 2 different email addys set in Thunderbird, though I plan to go back to just Eudora soon, as it has a few more options...(particularly, being able to set the time zone stamp to either the sender or the receiver.)
Thunderbird is very nice, but is not quite that complex yet...Pegasus mail 'might' be.