I free feed also. I know how much I put into the bowl each night for the following day, so that's not an issue. He's still been VERY food motivated. He just eats on and off through the day, so he's always plenty hungry to 'work' for food. He poos on a fairly regular schedule, so the house breaking has been not so bad. When I'm watching him, he has no accidents anymore. I free fed my previous shepherd for years. Especially if your pup is a "go, go, go" pup, it's hard to make sure they eat enough. I go give canned or cooked food every day, so that amount is subtracted from the amount of kibble he's given. He's used to having kibble available all the time. I've even given him bowls in his crate because there aren't any 'distractions' in there and he does eat better. Now with the larger crate, he'll have more room to actually eat in there. You have to adjust what you do based on "that" pup. As long as you're careful about monitoring weight and measuring food, you should be fine. If you find that your pup isn't interested in food for training, you can always just pick up the bowl an hour or two before training. My thought is that if the pup isn't responding to food rewards then you may not have the right reward.
Wrath of Grim z Dragon
"Mr. Grim"- Threaten my handler. I dare you.