The member discount is 25% off the rack rate. You'd have to call CRO/WDWTC to see if an AP rate were less expensive (or avavilable for your dates).
If you book your cash night(s) through MS, they will be linked to your points reservation. You wll not have to change rooms or check outr and back in again between the cash and points portions of your reservaiton.
If you book the AP rate, you may have to change rooms. At a minimum, you will have to go to the front desk and check out and back in again between the cash and points portions fo your stay. You may request to stay in the same room, but there are no guarantees.