If starting with a new database it is possible by designating a dimension in the account structure as the marker for the location.  This is done when going through the General Ledger > Setup process. 

For example:
An organization has three locations, one of which is a central office that handles all accounting.  The organizations account structure is AXX-XXXX-XX.  The first Dimension is designated for specifying the location.  In this example the designations are as follows.

01 - Central Office
02 - Location 2
03 - Location 3

Therefore accounts would begin with the number that designates the location.  For example, the user is entering an invoice for Location 2.  They would use an expense account that starts as A02-XXXX-XX.

This results in all accounts being created three times with a different location dimension.  Using this process will allow the users to enter transactions using accounts that will designate the location.  This will also allow the organization the ability to create reports bases on a specific location or all locations.

For more information, review the The General Ledger and Project Grant user guide.  You may want to contact the Blackbaud FundWare Professional Services department or your FundWare consultant to help with the setup to ensure that it meets your business needs.