This stuff just takes time. It was really confusing to me too at first, but after a lot of practicing the fretboard just kind of light up with the right notes when you think of a chord.

A good place to start though is to look at the chord shapes and pick single notes from there. In most cases, that won't be a true arpeggio with the notes all in order, but a good place to start because it would be easy to find. Try to find out which note is which within the chord - meaning - root, third, fifth, seventh etc. as you've already begun to do.