Under Preferences -> File -> Audio Data, I have Use Per-Project Audio Folders checked. I don't want anything in the Global Audio Folder (GAF), which I've deleted. Trouble is, X3 keeps re-creating the folder and shoveling the files in there anyway. Nothing is getting saved in the project folders I've assigned, even though I point to those files. Nor does it do any good to delete the GAF path in Preferences. It just re-assigns and creates it.
 
I'm working on a couple of hundred songs I've done over the years, and need the audio to stay with the respective project folders, not all lumped together in one gigantic directory.

Go to Preferences-Folder Locations and the the location for Project Files to the folder where you want it to save your projects, for example: e:\cakewalk\projects. Then when you save your project the first time using File-Save As, at the bottom of the Save As dialog, it will show that the Project File will default to e:\cakewalk\projects and the audio files for that project will be in e:\cakewalk\projects\audio or you could change those to wherever you want them to go. 

SONAR will not run without a Global Audio Folder. When SONAR starts up, if the Global Audio Folder specified Preferences > File > Audio Data is unreachable, the app will create the default location "C:\Cakewalk Projects" and reconfigure the application to use the default folder.
 
Trouble with the Global Audio Folder usually starts when it is configured to use removable media. The Global Audio Folder should always point to a fixed disk. In my case, I have the default "C:\Cakewalk Projects" defined as a directory join to the top of the directory tree containing my Cakewalk projects on another physical internal drive.
 
When creating projects using the per-project audio folder option make sure the Location path and Audio path in the "New Project File" dialog are defined correctly. Also pay attention to the Project and Audio Path entries at the bottom of the "Save As" dialog. When per-project audio folders are used properly, the Global Audio Folder will not contain any project audio data.

(Thunks me forehead.) I never thought of SAVE AS...
 
So here's what I did: I made a template and put it on the Desktop. Each song has its own folder on the F: drive, with an audio folder beneath each song folder. Each song has its files in the respective SONGXYZ/audio folder. I copy the template from the Desktop, paste it into a SONGXYZ folder, and rename it to whatever the song's name is. I didn't realize X3 was putting all of this stuff into the global audio folder. Now, I have to go back and re-save each song, pointing to the files in the SONGXYZ/audio folders. Major headache.
 
I looked at one of the .cwp files in a hex editor, hoping to do a simple FIND/REPLACE, but that info isn't included there.
 
 @scook: I'll double-check the Preference settings, but everything looks correct. Once again, I think the template I made is the culprit.

Yes, it sounds like the project creation method is the source of the problem.
 
Never worked that way myself. I use project templates but never actually copy the template into a project structure. When working with templates I work completely inside SONAR.
 
To work outside of SONAR using the example above would require a dummy project instead of a template. When a Cakewalk project is created using the per-project audio folder option and the per-project folder is nested in the project folder (the default), a relative path to the audio folder is stored in the project. This project file could be used as a "template" for creating future projects in the manner described in #4. FWIW, absolute paths are used when the per-project audio folder is not nested in the project folder.

What I had on my Desktop was a .cwp file. Changing it to a .cwt solved the problem of where Sonar expected the audio files to be. Double-click the template and SAVE AS to the project folder for whatever piece I'm working on.
 
Thanks, guys.