jmgi....I had the same problem, building up from the bottom instead of down. I solved this by putting the new box under the filled one. All mediums, it really isn't that much lifting. They built very slowly once I did that, so on my next inspection when I noticed the slowness, I swapped three of the outside frames, two from one side and one from the other, from the full box to the bottom empty box, putting them in the middle of that empty box. In no time they had the 3 empty frames in the originally full box drawn out and were building well on the new box.
I'm trying something new now as well. I bought a few sheets of cutcomb foundation, very clean/white, to use for starter strips. My latest body that I just put on the top has three narrow strips of this running vertically down from the starter strip to the bottom of the frame on each frame, sort of a vertical guide and ladder. At the bottom I just let it sit in the grove that's there. I rolled this foundation between a few pieces of kitchen parchment paper to flatten the embossing before putting it in the frame. But even if the girls feel compelled to follow that embossing, they'll be able to build whatever they like in all over the rest of the frame. This was my main reason for going foundationless as a hobbyist, just to let them do what they want. I'll let you know how it goes, I'm hoping to help my "straightness" factor this way as well. Wasn't bad on the first two boxes, but could've been better, we'll see.