With Komodo, the rocket is set up so each section burns out in sequence from bottom to top. That way staging is as easy as pressing one docking port when a particular piece runs out of fuel and it drops 3,000-10,000t sections away for me. Cos the engines are always on, I don't have to mess around.
It's much more efficient that way as well, cos I don't have unlit engines as dry mass on upper stages, they're all needed all the time