My advice to you is to design your home before you do anything. You want to make sure your foundation and bearing is adequate for the loads of the timber frame. Also the intermediate posts in the frame will need supports and footings in the basement, you want to make sure they are in the right places.
I am assuming you will be hiring someone to design the main house, so contact them now and have the house designed for two stages. Each state, and sometimes town, have different requirements for tie-down at the foundation. So it's very hard to give a blanket answer. Also the frame type will determine it as well. We don't use a timber sill beam, so we always drop the timber through the first floor framing to sit directly on the PT plate on top of the foundation wall. We use different connectors to tie it to the wall or floor girder.
We've had people contact us who have done what you are looking to do. A couple of them built their foundations without designing their home first, and the foundations couldn't be used for a timber frame. They had to build a conventionally framed home or bulk up the foundation.
So, design your house first, even the timber frame. If you don't it could cost you a lot more money when you do build.
