frame design for dummies

Although schooled as an engineer, I don't see myself ever producing a detailed frame design along with structural calculations and joinery details.  But when planning a timber frame home, some basic frame layout is part of the floor plan process.  

I'm planning a small (1,800 sf  +/-) timber frame home and the schematic design consists of three ‘boxes;’  a central entry core with a small wing to one side and a larger wing on the opposite side.  To make it easier to visualize, just consider a small square with a rectangle on either side.  

When laying out a preliminary framing plan (simple grid),  I treated the three boxes separately; but moving forward it seems wrong to have columns immediately adjacent to one another.  (the corner columns from two of the ‘boxes’)  

Question – is there any reason or situation where it would make sense to maintain the three boxes as separate structural systems?  (for a novice, it is much easier to consider each box separately)  Or would a real frame designer eventually remove the adjacent columns and design the overall framing plan as a single structure, not three separate boxes?