I don't have really good instructions for updating because I never have to do it the way a normal user does. (and I'm on Linux, not OS X or Windows).
But, there are other places you can put your content so that they're not stored in the Stepmania folder. Putting them somewhere else means you don't have to worry about the update method.
You can put your Songs, Themes, and other stuff in their respective folders in ~/Library/Application Support/StepMania 5/
(if that folder isn't right, then we'll have to get dbk2 in to update the wiki here)
That will keep them safe from anything that happens to the main StepMania folder.
Your preferences are in ~/Library/Preferences/StepMania 5/ and your stats and records are probably in there too. (the wiki isn't clear on this point).
Additional folders:
There's also the AdditionalSongFolders and AdditionalFolders preferences in Preferences.ini if you don't want to use the location mentioned above. Each of them is a comma separated list of folder names. Each folder named in AdditionalFolders is like having another Stepmania folder. Each folder named in AdditionalSongFolders is like having another Songs folder.
Moving songs:
If you move a song group from a normal Songs folder into a folder named in AddtionalSongFolders, you'll have to edit the Stats.xml of your MachineProfile and the LocalProfile that you play on to make the scores point to the right place. Song scores use the song dir to identify the song, so it's something like this:
<Song Dir='AdditionalSongs/Andy K-Pop Pack 2/Orange Caramel - Shanghai Romance/'>
This AdditonalSongs part is the part that has to be changed if a song is moved from one place to another. Be careful with the "find and replace" function in the editor you use, you might screw up the entry for a song that has "Songs" in the name.
