How do I record that I paid someone their commission?

Mark Paid records a payment you made — cash, check, payroll, however you pay people — against what the ledger says is owed. It does not send money anywhere. A paid row is never edited afterwards: if a payment later refunds, the ledger adds a negative row against the same charge so the history stays intact and the next payout nets it off; a correction works the same way. Commissions are computed from net amounts, so a refund never leaves a commission standing on money you gave back.