Generally when I start a new project it originates as a template or blank CWP both which I have created and then used
save as , There's no real difference between a Template or a CWP that looks like a template. .
I open the template ( CWP) and before I do anything I "save as" to the folder location I'm going to use and re name it.
I always check the
copy audio with project box. This is the best way for me and I've never lost audio this way.
I have a folder for each album with all the song folders inside that.
Each song folder contains the Audio folder, the CWP and the midi file. I also store the lyrics and the original as an mp3 if it's a cover tune.
I do have the Per Project box ticked in preferences but when you work like I do it's not even necessary. I'm more or less manually putting my projects in the folder I want it to be in. It's all in that crucial "save as" action. There's no difference in any software we use. Make folders and use them. Don't let software blindly stash things.
Some of my projects start as MIDI files which I open by double clicking the file. This opens Sonar and loads TTS-1 so you can get started. I immediately perform the save as to a CWP and browse to the new folder it will occupy. Always checking that
"Copy audio with project" box even when there's no audio involved yet. Did you make sure to check the advance option in preferences? The pre project box is there somewhere. But I don't trust it.