If you're talking about 2 separate DBs then you'll need separate BP Server instances. these instances can work side by side on the same machine if they are configured to use different ports. If you have a lot of resource PCs, then the recommendation is to limit the number to about 100, and if you need to go higher, consider getting a second server machine. If you're talking about both departtments sharing the same DB, then there is no real need to have separate instances of BP Server (assuming you're under the 100 resource limit). The ability to separate teams within the same DB is not possible yet.
