PicoC loads its script at boot time. I haven't planned to load scripts when flying (but it may be possible). Waypoints are loaded each point in their order. There ain't  conflicts, i think. Both combined offers more options (take a photo at a programmed point, wait a while and film a scene ...)
With enough recources, filesystem functions are also possible (log flight data, save waypoints when flying etc..). More ideas are welcome.
Separating into atomic partitions isn't the kings way, right?