In 100%, do you have to obtain every code before using it?

For example, is it necessary to do all the parts of box 1 - 2 before getting the time? Or all the parts of the overworld for world 3 (with the piano keys etc)?

100% means completing every puzzle, but not having to look at codes. So yes, you will have to solve every puzzle before the code, but you don't have to specifically look at the code. Hope this clears it up!