Can a customer have cards at two of my branches?

Yes, one per branch. A branch is its own restaurant here, so it runs its own programme with its own goal, reward and stamps — a card earned at the marina does not spend at the airport. Cross-branch shared cards are deliberately not a thing: each branch's reward liability stays its own, which is also what makes the branches screen's revenue comparison mean anything. If you want one shared programme across outlets, that is a single restaurant with one menu, not a group.