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When I create a session the song title appears next to a folder. In the folder I will have the song title again next to the Protool icon, and obviously thats my session with tracks and all.

There are some other items in the folder-

Audio Files Folder
Session File Backups
Wave Cache.wfm

What are these and what are they used for?

Audio Files: all the audio files for your project live in here. this is so you can easily transfer your project between computers.

Session File Backups: pro tools automatically saves back ups of your projects every so often, so if you have a crash you can restore your project.

Wave Cache: wave cache files.

Really appreciate it.

This leads to my next greenhorn question. When I open my external hard drive, I seem to be creating sessions in two different ways and things are starting to look sloppy.

1. Song title "A" next to a folder icon.
2. Song title "A" next to PT icon.

I'm assuming #1 is the correct view of a created session. Maybe #2 is the result of doing a "save as" and not putting it in the correct folder?

Guess the question is, do I want to see just folders when I open my external hard drive?

That is most likely what has happened.

When you choose Save As from the File menu, it is only saving the Session File (not the entire Session Folder and all of it's contents).

You can store your files any way you wish, but from a file management standpoint, yes, you would probably want all of your session files within their respective session folders. It would be all to easy for pieces to get lost/separated if they are in different locations.

You can also create folders within your session folder to organize your Session Files (for example, I often create an "Old Sessions" folder within my main session folder to store all of my older versions of sessions just in case I want to go back to where I was at an earlier point during production)