The Night Audit function is a daily audit of all transactions and booking activity for the day. The Night Audit process reviews and catches any errors, bookings that are missing information for the day, charges Room Rent to each Folio, and then increments the system date. This includes Arrivals, Departures, Unbalanced, and Group Folios. There is no required time that you must run night audit. Some properties run the Night Audit at the end of day, at night or early the next morning. Some properties run their property as an Auto Night Audit process, at times they set and this auto-increments the System Date, settles credit cards, may auth arrivals for the first day's rate, and emails any 'errors' to the Property for fixing later. See this article for a detailed discussion on Auto Night Audit vs manual Night Audit. And if you wish to auto-batch pending credit card payments/credits, and/or automatically pre-authorize credit cards for the first night's rate for future arrivals as part of your Night Audit process, review the documentation here. The Night Audit Process starts with a check list of items that must be completed before Folios can be charged and the date incremented. See details of each step below. The last step of the Night Audit Process is to Increment the Date of the System, which appears in the upper, right hand corner of MyPMS. See Page Header. 
See video tutorial MyPMS:Night Audit Screen | 
There is an option to not allow Night Audit to be complete while any credit cards are un-settled, consider making 'Settle Credit Cards' a part of your Night Audit routine by making that a requirement in the PMS Setup area.