I'd say the water shuttle starts at 08:30am. I remember taking it one morning and was still at the gate before the parks opened. There is a boat dock near the conference rooms. The shuttle lets off in the middle of CityWalk, about a 5 minute walk away from either park.
The walking path follows the water way. It takes about 7 minutes if you walk. The path exits next to Margaritaville, leaving your a very short walk to IOA, slightly farther to USF.
I'd say you can take the walking path in the morning, and then take the boat back in the afternoon when the kids feet are tired.