An easy way to keep them separate is to have a separate computer for each database. Computer 1 would synchronize Database A, and Computer 2 would synchronize Database B, Computer 3 would synchronize Database C, etc.
Database A |
Database B |
Database C |
These computers can be on the same network, but should only be set up to synchronize with the appropriate database. For example, the three Chicago computers could be connected. Chicago Computer 1 would synchronize Database A, and Chicago Computer 2 would synchronize Database B, Chicago Computer 3 would synchronize Database C.