So i looked around and from what i can tell you cannot remove personal email from your messaging folder. I am currently running a BES device and i have personal email going to it aswell. Does anyone know of a way to have my personal email ONLY going into my personal email in box??

There is a code update for BES that will create a BES only mailbox. Unfortunately not many BES admins (myself included) won't deploy this just yet as there are limitations. Presently you cannot name the mailbox so the folder will be labeled "desktop" so it would just cause confusion to users.

ah well that makes sense, but just to confirm there is no way to remove my personal email messages from showing up in my general "messages" folder

Nope. All messages will show up in Messages (unless you have separated SMS/MMS).

could you please give a little more info on this "code" please

If your device is running OS 4.3 then you can use Empower BES Mailbox...gives you a view of your Messages mailbox that only shows work email.

My wife uses it and likes it very much. But...not compatible w/OS 4.5.

To enable this on your BES it needs to be 4.1 SP5 or higher and the BB OS needs to be 4.1+

Reference KB15003 at Blackberry support.