Marbles are earned by finding Secrets: one for each secret filed in your ledger, and nothing else. The ledger already holds them, so forgetting the ledger forgets the marbles too. They are spent at the shop’s counter, kept in your own browser, never bought with money and never exchanged for Sardines or Thimbles.
Ferrule pays in marbles: in Always On she gives you the cat’s eye, the best thing she owns, for bringing her bell back. The shop’s marbles are not hers. Where they come from instead is the things that hide.