Do I have to put the Room (Accommodation) Charge on manually?

No, this is done automatically after the Night Audit has run. When the Night Audit runs it will post the accommodation (room) charges for all checked in rooms. You only need to post the payment against it (when the guest has paid), so the balance is 0.00 and you can check the guest out.

If the Night Audit has failed due to a missed check in/check out and is now on the wrong date (the day before), then you would need to manually run the Night Audit so the charges can be added to the rooms for accommodation. Firstly, you would need to check the guest in or not (the one that has caused the Night Audit not to run) and then go to Administration > Property and you'll see Manual Night Audit, click the "Start Night Audit" button underneath this. Once this has run, the accommodation charges will be put on the rooms.