Sorry I didn't respond here earlier. Missed the thread.
Im not saying im some sort of gury to file management but here's a few things to consider.
Never trust any software to name your files for you. One thing all software has in common is the "save as" button. The save as, allows you to save a file as whatever name YOU want. So after recording one ore more tracks at once, you start saving it by double clicking on the first track which puts the track (or wav file) in the wav editor. In there you can saveas whatever filename you want. Then when you go back to multitrack view the wav file is still in the same track but now its called "overhead drum 1" or "vocal a" or something. Save all your tracks this way and then save your session (mix file). Having logical and descriptive names for your wav files makes it easier to know whats going on and easier to back up as well. I always set up folders from the main mix folder for the given song. Folders like drums, guitar, vocals, bass, etc. And then make sure my drum tracks are named apropriately and saved in the apropriate folder as well. When I make a change to the Track (file), I will save that as "overhead drum 1_ed". I never save over the original wav takes. That way I can always go back and start again with the mix without having to re-record. And I will know exactly where to look for it since I named it with a more obvious name like "vocal b.wav" instead of trying to find a track called "track 19 (7).wav" which you would have to listen to if you want to know what it is. In cooledit 1 and 2, you can name the tracks in multitrack view before you record. That way when you double click the track (wav file) into the wav editor to save, it will already default to the track name in the saveas dialogue. Second and third takes might look like this:
overhead drum 1 .wav
overhead drum 1 (2).wav
overhead drum 1 (3).wav
So just remove the (2) and saveas in the apropriate folder.
D:/songs/threeblingmice/drums/overhead drum 1.wav
When you finish recording you save the mix. And nothing happens apart from the fact that you save the mix. However when you go to exit the program, it asks if you want to save all these other tracks, or takes. They will be files with bracketed numbers in them. Say no to all and exit cooledit. Then restart cooledit and load you mix up again. Check in your orginiser window that the wavs are saved in the right folders by clicking on show full path. Just to check that everthings in order.
Now you have an orginised mix. When backing up the mix you can save the drums and guitar on one cd and the bass and vocals and mix files on another cd and so on. This makes it a breeze to bring back mixes from cd backup. Since the entire setup can be viewed in explorer.
I have a template.ses file that has the 7 or 8 drum tracks already named and setup to record drums. Its actually an entire folder setup as well. That way half the works done before I even start.
This is the way that I work and its very simple and I haven't lost a track ever. I recently loaded up a few songs I had backed up from a few months ago to redo some guitars. They loaded up perfectly and I even had some presets saved and notes about the mix to go on. Simple.
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, I'll assume you know what you're talking about.