I think 'automatic syncing' would be convenient, or maybe a popup ("Send this to the cloud?", "load your waypoints from the cloud first?").
Not just for waypoints, but also for aircraft and settings.
I've tried to train myself to "load waypoints; edit; save waypoints", so that the cloud always has the "best" setup, but I'm not very good at it yet. (OTOH, I don't add waypoints very often, and my existing ones don't actually change, apart from trying to get consistent in my choice of icons.)
An alternative could be that when I'm updating the charts once a month (but presumably it checks every startup?) it could ask that the cloud-settings (waypoints, airplanes, personal limits, etc.) have been updated, and if I want to override my local settings with them.