If you go into Profiles<Advanced, you can pick the profile that you use, and you can set the e-mail notification to none, then you won't be notified when a new e-mail comes thru.
Or, you can log-in to the BIS website > choose the email address in question > choose FILTERS > select Do not forward messages to device. This worked perfectly for me. Then you can go back and turn it on anytime you wish.
One thing to note is that the filters are not available on the BB itself (which doesn't make a lot of sense) unless you use a 3rd party browser such as Opera. If you use Opera you can just log-in to the BIS website from there as if you were on a PC.