It is by RIM design that the BB cannot wirelessly sync to one source like your corporate BES/mailbox and sync non-wirelessly with desktop manager. Long story short, the PIM data the user wants to sync will need to be set to NOT wireless synch.
Let's take contacts for example - you could either use the handheld to go into address book > options > wireless sync: NO or edit the PIM sync settings on the users account from BES. Once the selected items (contacts, calendar, notes, tasks etc.) have been configured for non-wireless, the user will need to physically sync their BB with desktop manager at work and home.
~ CFJ