So .prj was the extension used in previous TestStand projects, and that became .tpj, correct?
Also, what is the .tso file created when I create a new workspace and project file.
Finally, are there any suggested templates for good project/workspace organization?
The .tso file contains some of the options and properties of the Workspace such as the version of TestStand used to create it, and whether the trees should be expanded or not. You can open both the .tso and .tsw with a text editor to see what they contains.
There isn't a recommended template on how to organize your workspace and project. The structure will be application dependent. As long as you believe it is helpful and contains all the files you need you should be fine.