I just looked at the Evolution FAQs. I saw this:
Is it possible to have separate individual pop accounts?
This is not possible, Evolution only has one unique inbox for incoming email. Either use IMAP instead of POP or move incoming emails into different folders by setting up filters: set up a new folder and create two subfolders (for incoming and for sent mail of that account). Now set up an incoming filter ("Edit > Message Filters...") to move incoming mail to the incoming folder by filtering on the recipient's address and an outgoing filter to move outgoing mail to the sent folder by filtering on the sender's address.
The version of Evolution I am using is 220.127.116.11 on Debian 5 "Lenny." I am not sure how the Ubuntu version does, but it is probably similar. Perhaps someone who uses both Evolution and POP3 can give further advice. Also, you may wish to post this question over in the Ubuntu forums since Evolution is installed by default over there, whereas Thunderbird is the default over here. Good luck.