They traded with spices (Season 3) and with goods. They had to pay the automated repair station (I forget with what). I'd say they were paid, but we didn't see anyone really talking about it.
Perhaps that was a missing Season 5 story - Mayweather Gets Audited.
They had to pay the ARS with something. Even if they did have money, the Federation didn't exist yet and it would have been Earth money - with no interstellar value.