If you are planning to use the Disney transportation system while you are at Pop Century, all you have to do is get your free parking pass when you check in, park your car where you want it to stay for the rest of your trip and then don't bother with it until you are leaving.
However, because you are a resort guest, if you choose to drive to a park, your parking there is also free. Just show your Pop Century parking pass and you'll be waved through.