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.