I'm assuming "per project" audio will mean saving projects as "cakewalk bundles"No its NOT a .bun file.
It just puts all the audio for the project in the Audio folder, and that resides in the Project folder.
<folder>
My songcontains
My Song.cwpand the <folder>
Audio that contains all the wav files for the project.
Now if I want to copy/move the project I can "pickup" the folder and "drop" it anywhere I like.
ie. Thumb drive to take it to another machine, an internal backup drive, or my external backup drive.
I would suggest opening each project and do a "save as" and tick the box that creates the Audio folder,
then tick the box that copies all audio to that audio folder.
Storing all the audio in one "Master" Audio folder (one that includes all the wave files for every cwp);
is a recipe for disaster, at least in my opinion/experience.
As to your midi question:
I leave all midi in a track folder named MIDI and then I archive that folder after freezing all midi tracks.
Just the midi is there, the frozen tracks are now wav files and have there own track for mixing.
If I want to revisit the drums, keys or bass; I can unfreeze and edit those tracks.
HTH,
T