Yes, for sure each song should have it's own folder. 
And as far as I can see simply naming your tracks clearly and in my case I even date them when naming. 
Vocals Sept 3- take 1 . 
So very easy to keep things straight. 
Good tip to always save every project as a MID. file.. a lot of my hardest work goes into midi tracks.. I can always re sing or play the guitar parts. 
 
I find it hard to believe that anyone could fill up a modern TB hard drive these days.. I guess if your using 198HZ. 

I am understanding that ORGANIZATION is key here.  I think I am getting off the mark at the very beginning when I SAVE a project.  I am not giving Sonar any direction as to where to save the .cwp file or the audio files.  I think the beginning is the key to all of this.
 
Thanks to all who have replied.

Preferences  > File > Folder Locations
 
The very first entry is the root folder where your projects will be saved.
 
All of my projects are subsets of this root folder

I answered your PM but I'll repeat here as it might help other's too. 
 
First off, I don't like Sonars default set up as it certainly leads to problems as time goes by and as one goes looking for files. 
I treat Sonar like any software I use... Even MS Word will automatically stash everything in the Document folder.. After 100 documents you will certainly have trouble finding that favorite recipe. 
 
So the solution for all data storage and organization is simple- FOLDERS. 
 
My system is simple but it would seem by the fact that this thread subject comes up at least once a week it's worth repeating again. 
 
I store all Sonar projects on a data drive**. As that drive is 100% for music I keep my "Album" Sonar folders at the top of the tree. If you open that drive you will see folders named for each Album, be it a  Live band,  Client or Original song ideas etc. There are a few other folders for MP'3 , MIDI and lyrics.  
**Note: On my laptop I don't have that option so I actually use the default Cakewalk Projects folder. But inside that folder is the same idea, folders for albums etc. 
 
Inside these Album folders is a folder for each song ( project). 
Inside each song folder is the CWP, MID, Audio folder, Lyrics ( now the Mix Recall folder . I might have a few versions of the song and the lyrics and various scratch versions or the original cover song. 
So I can copy the entire album to a back up drive for both safe keeping or in the case of the laptop, I record live gigs and transfer to my main DAW. Been working this way for ever and have never lost a song or an audio file. 
I date the Album folders so I will know my last back up and versions. 
 
DRIVE F-/
              Sock Monkey-/ 
                                   Blackberry-/ 
                                               Blackberry  CWP
                                               Blackberry  MID. 
                                               Blackberry live WAV. 
                                               Audio Folder 
                                               Mix Recall  
                                                

Deleting unused files have no effect to SONAR.
We digitaze tapes and vinyl and have audio data with 100 GB and more (over 100 hours of tape) per project.
There are even 1000 of clips..
We don't run out of memory although we have only 8 GB RAM.
When the project is finished we do the command "Clean audio folder" and archive the project.
SONAR can handle large files and even over 100 hours audio in one project without any problem.