When I use the TIO to just set a stone or two, I put the stones in one layer of TIO and cure and then add another layer of of TIO going around the stones (not over) to kind of build up a "lip" around each stone. However in a full crystal nail, I would use the Structure without the TIO. Since it is thicker, you can lay down a thicker layer for the stones to sit in. I do use it to embed things all the time with success.
It would be very difficult to lay down TIO on a crystal nail without getting it all over the crystals.