Proper Mailbox Setup Across Multiple Computers and OS's

What is the proper setup of a persons Mailboxs and Folders to Keep from repeating items as new in opening on another computer or OS.

I swap back and forth during the week from Lion, and Snow Leopard on a New Mac Mini. Snow Leopard Booting from an External. I have to set up mail in each OS as the actual programs are not compatible. So I have created the same folders and Mail boxes. I also have items directly sent to folders when recieved which meets the rules sent. I check the new email from these folders. The Folder reside on MOBILE ME. But as each Mail Program is Launched it will grab the messages again off the server as they run independant of the other one.- even thought they both are set to drop new messages into the same Folders on Mobil Me. Thanks for any help. I'll hit you all up again when Mobil Me closes as I think your going to direct me to this as the bridge to link them all together.