Assuming that I am understanding your situation properly, I would attack the problem using system tree location as you have already segregated the systems
In your assignment rules, assign My Org\location B to the Agent Handler and remove the ePO server from the "Handler Priority" list altogether. You will get a warning "Warning: The custom handler list does not contain the primary agent handler". Just ignore the warning.
Then create another rule that assigns the systems in My Org\Location A to the ePO server.
Hopefully this helps ya.