Current builds of RIM's do have separate inboxes for BES and BIS mail--assuming the option is enabled by a BES administrator--in addition to the main "Messages" inbox, which by default collects all e-mail sent to your device, regardless of which account it was sent to.
If you're running a recent OS 5.0 build, separating your BIS and BES mail could be quite simple. And even if you're not running the latest BlackBerry 5.0 OS, I've got a trick for you that'll also create separate BIS and BES mailboxes.
I recently installed a leaked version of BlackBerry OS 5.0 (5.0.0.586) on my , and I was extremely pleased to see that a new icon for my BES mail appeared on its own. I've since upgraded again to OS 5.0.0.593, and this build also has the BES-specific icon, but previous builds, including the official T-Mobile OS (5.0.0.330), did not seem to have this corporate mail icon. (I'm told that to separate BIS/BES mail, as well, regardless of your OS version. So it might be a good idea to check in with IT, if you don't see separate icons on your BES-enabled BlackBerry.)
To find out if you already have separate inboxes for your e-mail accounts, first ensure that your device is connected to your organization's BES. Then go to your main BlackBerry "home screen" by clicking your BlackBerry Menu key--directly to the left of your trackball/trackpad. On the home screen, click Menu again and ensure the "Show All" option is checked. This will make sure that no e-mail inboxes are hidden.
With all icons visible, look around your home screen for any and all e-mail-inbox icons. You should see the main "Messages" inbox, along with icons for every BIS, or Web mail, account. And if you're running a recent OS 5.0 build and/or the option is enabled on your BES, you'll see a BES icon, called something like "Desktop" or whatever you've assigned as a label for your corporate mailbox.
Your mail is already separated if you see the BES icon--it has a small "briefcase" at its base, as opposed to the BIS icon, which has a small globe. Ensure that none of the individual mail-inboxes is "hidden"--hidden icons are "shadowed" or more lightly colored than visible icons. If one icon is hidden, scroll over it, hit your Menu key again and uncheck the "Hide" option.
When no e-mail inbox icons are hidden, click Menu one last time and uncheck "Show All." You may also want to hide your main Messages inbox, since you'll already have separate inboxes for all accounts.
I prefer to use a "Today" theme that has fixed "Messages" and "Calendar" sections on the Today screen, so I can access the Messages folder from there, even though I have it hidden on the Home screen. And I keep separate inboxes for all my mail accounts on that Home screen for quick access to specific mail. ( for the Bold 9700 is one example of such a theme, and it's also the theme pictured in this post.)
If for whatever reason you do not see a specific e-mail inbox for your corporate BES mail, no worries; you can still create separate inboxes on your own.
Just open up any mailbox, hit the BlackBerry Menu key, scroll down to and click Options, then click "Inbox Settings." On the Inbox Settings screen, uncheck all the listings for your Web mail accounts. In other words, you want to uncheck any and all mail accounts that are not your BES mail, so only corporate mail appears in the Messages folder. You should also uncheck "SMS and MMS" beneath the "Other Message Types" heading, so the main Messages inbox collects only your BES mail. By doing so, you're making the default Messages folder your new BES-specific inbox.
Depending on your specific app-settings, some non-BES messages may still appear in the Messages inbox, like chats. But you can modify settings within those apps to remove chats/notifications/etc. from your now-BES-specific Messages folder, as well.
Voila. You should now have separate e-mail inboxes for your BIS and BES accounts.
Check out my for more BlackBerry tips and tricks.