Ordinarily, treat the whole structure as a complete structure, unless you want to do some sort of a double, banded post and beam system, which would be really interesting to see, but maybe not the traditional look you might be referencing.
For your first timber frame, especially if you are using as is or hewn material, I would recommend working off of centerlines for all of your layout, and try to have all of your components relate to each other in some way. All layouts in the house divisible by 18", for example, also provides a nice framework within which to design. If there is a mathematical underpinning logic to your design, then mistakes in the field are minimized because you have set up an early warning system for your spidy sense, if you know what I mean. If you are used to seeing nothing but 15's and 30's and 36's and suddenly you are getting measurements of 28's and 32's, you instantly know that something is not right.
Of course, the details of the design will be driven by your available materials, so, sometimes, the 3 box system might be the way to go. If none of your timbers are big enough to deal with the loads, and you are going to have to laminate anyway, then individual boxes start looking viable. And, if you already have a mish mash of material, then maybe you can't even utilize a nice clean mathematical grid either, but that might be a 2nd or 3rd timber frame project, instead of a 1st.
Cheers, Chuck
