Hey Toluca,
The trick is to design both frame and floor plan simultaneously. I would recommend consulting an experienced architectural/timber frame designer. It takes a lot of experience and practice not to menttion and almost instinctive understanding of the strengths of the timber frame material you're using and the loads involved in the application. Once you have that then it just a game of Tetris!
I am frequently presented with a client's floor plan design and asked to build a timber frame for it. It takes a great deal of gentle diplomacy and mental gymnastics to make it happen. It is an iterative process where you design, redesign, and let the design grow. you can't rush design, but when you get it you find things start falling into place and all of a sudden all of the puzzle pieces fit! It's really pretty remarkable how a design can seemingly take on a life of its own and suddenly mature. But it can take time, sometimes you have to work feverishly, and then set it aside for weeks or even months and then come back and see how its going. Its not like the design changed, but somehow your mind needs to forget some of the restrictions it developed in order to be open to the solution.
It's thrilling to see it come together, but even better is the relief and joy you see as your client's struggle with what at times has seemed like an unsolveable brain teaser is resolved.
What a great business this is!