Hi Donner, I agree having the ores and coal able to be locked based on the total gathered would be a great idea, and its been a suggested before many times.
My clans citadel is now fully maxed, so we don't have this issue any longer, but during the time we were building up the citadel we used to get targets for coal and ores at a few thousand at a time, but it needed to be monitored daily. Also educating classmates so that they could understand when we needed more ores or coal helped, and shared the responsibility with everyone . That way we didn't need to worry too much about having over capping or not reaching targets.
Kera:
Proud leader of Shattered Moon