So, if I want to "save" anything (documents, etc.) I have to run the save command manually? Or is that just changes to system files?
Yes. To save anything to a protected partition, you'll have to "commit" manually. This include system and user files. Of course, you can save files to a different, unprotected partition just fine.
But, if I wanted to do something like run Eraser to clean up the drive, I could disable the RAM overlay from the command line, then run Eraser, re-enable the overlay, commit and save. Is that right? Or, am I still off?
Not quite. It seems that options like enable, disable and commit happens at shutdown / next boot. So, from an enabled state, you have to:
2. Reboot. From this boot, the partition is unprotected.
3. Run eraser.
5. Reboot. From this boot, the partition is protected again.
But anyways I don't see the point of using eraser, since the disk is only written to during commits, i.e. the shutdown process after running a "-commit" command. Doing manual TRIM with eraser may speed up this process, but it doesn't speed up general usage.