Currently, there is no distinction between transactions that were made in Bookkeeping and which were made on the front end of the site.

As a workaround, the user can add a custom field to the Sphere Entry forms.  Sphere Entry forms are only used through Bookkeeping, so if the user adds a custom field that has to be filled out with each backed end transaction.  When the user runs a report, they can filter on all transactions that have or don't have that field, therefore distinguishing between Bookkeeping transactions and front end transactions.