I think making matrices or flow charts aren't conducive to how i think, personally. I like to make a straightforward, linear concept of how each character's personal plot might go and then organically evolve it and interlace it with other characters or the main plot. Maybe I decided that one session that character A's father is the same merchant that employed character B, so there's a connection. Maybe the archnemesis of character C is that same guy I planned on as a foil in the main plot. It's pretty close to how I plan the main storyline - I think of beats, NPCs, and specific events, but I leave things open so that players can feel like their decisions are driving things.