I'm on an older version of Desktop Manager, and don't have a similar setup but here are some things I'd try:
1. Synchronize>Configuration tab>Configure synch>Select "Choose" for address book>there should be an option near the bottom that asks for folder name. However I think you can only select one folder?
2. Synchronize>Configuration tab>Configure synch>click on the "Configure" drop down menu>advanced>filters -- set up a filter. I'm not sure how your contacts are arranged, but if the different folders also coincide with different categories, you can select specific categories for desktop manager to synch over to your BlackBerry.
I'm a bit more familiar with the second option as I have 2 BBs at home using the same Outlook profile. But the second BB device only synchs a portion of the entire address book.
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