we are facing the same thing. Our youngest is also 3 and EXTREMELY active. We have bought a leash and wonder if she will let us use it at all. She doesn't like to hold hands or anything... wants to do everything by herself. We are going for 7 days, and I am a little concerned.
We have limited the sit down meals we are going to do to 5 (including breakfast, lunch, dinner) right now and then see how that goes. We have breakfast PS at Crystal Palace, and will do a Fantasmic dinner (probably at buffet), and three other dinners. The ones we have chosen all have some sort of entertainment aspect, so hopefully that will help. We have picked Marrakesh that has belly dancers and Biergarten with oompah band in Epcot, and we have also picked Ohana that has the coconut races and hula hoop stuff to watch the fireworks at MK. I really want to also do a breakfast or two at the resort restaurant (Boatwrights), but will make PS's along the way. Our little one is a little too active to do restaurants really well, but I am hopeful that the entertainment will help.
Other than that we are going to attempt to not do commando, although we will go to the parks every day, and stuff. We will take a break every afternoon to let everyone cool off and calm down.
On a side note, is yours potty trained? I keep going back and forth regarding this issue. Ours is, however, I don't want to be worried about this the whole trip. My fear is we will be in line about to go on a ride, or on a ride and she decides she needs to go. I am debating putting her back in pull ups while in the parks with a lot of rides (mainly in MK), but leaving her out when we are just going to be wandering around a park or doing very few rides with short lines (Epcot at night - Animal Kingdom), and forcing the potty breaks then. I just don't want her to revert. We have to do pull ups at night still, but just wondering about taking a chance during the day.