But I'm not sure how to fill the gap between secondary routes. My last trip involved traveling SR 729 north of Culpeper, but I don't know how I would write that in my .list file.
Without even a draft route file to look up for that segment of SR 729, you'd be guessing not only the waypoint names, but also how the route would be file-named to distinguish it from any other SR 729s in Virginia. You might do better to log your non-TM-mappable travels in a separate file from your list file, so you can use whatever format you prefer.
I have such a separate file with draft list file entries and other notes for routes that I expect one day to show up in TM. (But I don't even track Virginia SRs, or county or other local routes in other states.) When it's time to move draft entries into my list file as new systems are added, I often find that I've guessed wrong on how the route or its waypoints will be named or which points are included in the route file, so I need to redo entries anyway.