If you stay onsite ONE night, you will get TWO full days of Express passes. If you stay onsite TWO nights, you will get THREE ful days of Express passes. So, if you want to do a 3 day/3 night trip, I suggest checking in on your first day you want to visit the parks. Spend two nights in the hotel. Then, on your third day of visiting the parks, wake up, check out, and load up the car with all your stuff. Then go and enjoy the parks. Once the parks close (or you are ready to leave) take the boat back to the hotel, jump in the car and check in to an offsite hotel to save some money.
If you have the time, and can afford it, I would go for 3 days and stay onsite for 2. Of course, if you can afford it, staying onsite for 3 will make your trip more relaxed since you will not have to move around from hotel to hotel.
Of course, it also depends on when you are traveling. If you are going when schools are out or around a holiday, three days will be needed. If not, then you could manage with only two days, but its always nice to have that 3rd day to see anything you might have missed!