Both Disney and Universal hotels have special rooms where they can hold your luggage, so i would just plan the move around my day, and give them a call to let them know if you will be arriving after the hotel check in time so they know you will be coming. Call the hotels first to get the check in times and ask what services are available. I believe they will give you your park passes at any time during the day, and may even have special rooms you can change clothes in etc.