By design you are not able to see emails within sub folders after an Enterprise Activation. Once your device is activated and new emails arrive in sub folders (or you file them from the device) they will be visible on the handset. As a work around (you must have BES 4.1.5 or higher) you can do the following:

1. Open Messages
2. Press menu and select Search
3. In the Search Type (top right) menu select Remote
4. In the search properties select the sub folder you require and then any required variables (e.g. name, subject etc) or leave it blank to retrieve all emails
5. Press menu and select Search
6. After a few moments you search results will be returned in lots of 25 emails (you can press menu and select to retrieve more if required)