When you save project:
Result:
You name project 1 so project and media will be in folder 1.
or...
Result: you import or save project name 2, project will be in folder named 2 and media will be in media folder. Experiment.
Secondary path is I think exclusively for per track recording. Right click Record arm button on track panel and go to track recording settings. Down there you can set primary or secondary path for this track recordings.
I always thought this should be more clear.
edit:
I am sorry. You meant a projects. These settings guys already show should work.