remember your first save is the most important one.
when you make your first save, begin a project, make sure that folder is set where you want it.
Also be sure to check off the Save with Project option.
I have been saving the same way for a long time now, so my habits aren't the best but they are productive.
In my project folder, I create a file with my project name and inside that folder I create another file called: Audio.
I do all this before I even start a project. This way when I start my project, I simply navigate to this folder.
Your options now are simple really. open the project and do a "Save as". with the audio folder checked.
then you can run the "Cakewalk Clean audio folder".
I do this after I bounce all my track "Bounce to clips". this makes my folders more manageable.