I've made a mess of my files and I'm trying to consolidate everything for my new demo into one location that can be easily backed up. My question - does checking the per project audio option override the project files and global audio folder pathways?  For some reason (user error) many of my audio files are on my secondary drive, but all of the per project audio stuff that I've saved is in the cakewalk project folders on my c drive. 
I'd like everything to be on my secondary drive, but how can I port everything over and make sure that I can still open all of my projects.   What is the best way to set up per project audio (and convert all of my messy files) for my secondary drive?  I'd like to learn the most efficient and streamlined way to do this.
Thanks in advance. 

I would open each project and "save as" to another location with the copy audio option enabled. This will give you per project audio in that location which as you now know, you should have been doing anyway.

I always use the Per Project Audio folder. It creates a folder and places the audio folder and the project data into it.
 
Sonar should want to create new stuff in the C drive in the Cakewalk Projects folder. At least mine does. Once I finish a project, I will however, cut and paste it (the project folder) to my storage drive. I mirror that one to my external storage as well.
 
Now.... 6 months later, say I wish to open the old "moved" file to work on that song again. All I do is navigate to that folder on the storage drive, find it, click it, and it opens and runs from there. No need to move it to work on it. All saving is done to it's new location on the storage drive.
 
So.... while it may be "pretty" to have everything in one place, the computer doesn't care where the project is as long as it can see it.
 
I use the Cakewalk Project folder for the current songs I am working on, and then in the storage drive, I have folders indicated by name for the year the song projects were placed there. So I can search "Songs 2010" for the songs I completed in that year.... but it's over on the storage drive....
 
One more thing.... I believe the per project audio folder is active by default. So unless you changed it, you should have Sonar creating the preferred method of storing the audio and date already....