The way I do it pretty much like the above mentioned.  The computer I use most often, I have the settings "leave mail on server," activated.  This way, I'm sure that when I check on the other computer (usually after a couple days or so) it will have all email.  Also, check the remove from server email computer immediately after you check on your leave on server computer. This way, you're pretty much guaranteed that it wouln't remove anything the other doesn't have.
This might be a little confusing, but it works.