I’d like to keep some notes about a song, like the number of cents to add to get the recording in tune. Makes sense to keep it somewhere in AnyTune, and part of the song information, so it gets backed-up, transferred to another device, etc.
Pretty much any data that you apply to a song is saved in Anytune. So, for example if you set a song to a particular pitch, change songs, change the pitch on the new song and then return to the previous one, then Anytune will recall the pitch setting for you. All of that type of data is backed up when you sync your iPad.
To your specific question about notes – you have 2 choices.
From the All Tunes list, if you tap the info button next to a track, you can bring up an editor that will let you add a note to the track. When you then change to that track, the note will be visible as a pop up that appears over top of the big waveform. It will also show up under the song in the song listing.
Alternatively, you could add a mark at the beginning of the track and then change the mark text to indicate whatever information you want.