The mailbox agent is an assigned thread manager for communications of BlackBerry devices. Each mail server is assigned to a particular agent, so all users on MAILSRVR1 will be assigned to the same mailbox agent. The highest number agent, by default, is 5 ...however, you can break a user to their own agent by defining it in their properties - these start at 200 and up.
Best practice depends on how many message servers you have. RIM recommends a one-to-one relationship between messaging server and BES server, although that's not entirely feasible for some companies. With that said, in a 40 messaging server and 8 BES server environment, I would recommend assigning users on MAILSRVR1-MAILSRVR5 to BESSRVR1, MAILSRVR6-MAILSRVR10 to BESSRVR2, etc. This would give a one-to-one relationship between messaging server and BES mailbox agent. If you have a BES server that is managing users on 40 messaging servers (roughly 8 mail servers managed per agent), then you run into a massive spaghetti incident that will end up causing overstrain on the BES server and its agents/threads, thus causing quite the headache for users.
What kind of environment do you have (messaging servers, BES servers)? It's best to look at that and assess how you want to configure your BES and its agents.
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