How to add marker positions to audio metadata in ffmpeg?
What you are talking about are often referred to as cue points. These markers are saved in a "cue sheet" which is a separate file that contains them. These cue sheets are recognized by several audio players.
You don't mention what format you want to add marker positions - and the only format that I know that have them built in are iTunes audio book files. They call them "index markers" and I don't know of any available tools that support them.