Can I charge a deposit for a reservation and charge the remainder when the guest checks in?

No, you can't charge a deposit for a reservation and charge the remainder when the guest checks in. The price you set when setting up your Reservation Types, will be the amount the guest is charged 48 hours before the reservation date. 

NEW: Reservations will now auto-capture payment WITHOUT a host assigned. For more details on how reservations are charged in Commerce7, please click here.