I give each project a folder - in it are subfolder - Architectural and Timberframe. Within the TF folder I use Engineering and Shop Drawing sub folders to keep everything sorted.

Depending on the size of the frame you could end up with lots of part drawings - which will clutter up your files so I keep these sperate and uniquely named.

A '.skp' file is no different than a Word, Excel, or PDF file - they can live anywhere convenient to you.

Out of convenience Clark suggests building a unique folder / location for your TF joint and timber components. This allows you to easily find and reuse common parts... Some of these may be the same as the parts in your current project - so be sure to have a good naming system so you an find things on the next project - or 5 projects down the road.