my desktop speakers are a 2.1 set-up. my audio output goes to the subwoofer and then a 3.5mm jack outputs to the 2 speakers.
never even thought of it, but might be able to plug headphones into that sub output and have it work like you are thinking (or at least what it sounds like you are thinking). sub would do its thing and the rest would go to the headphones.
again never even considered such a thing, but the theory sounds right. otherwise, you'd have to have separate outputs for each. no idea how that would wire or if it would or would not work, but that would be the basic idea.