I don't keep ducks (only chickens) but have this year, switched to using wood chips (not shavings) as my coop bedding and run ground covering and found it to be a good odor/mud/etc management method. You may need to run a rake across it every so often (chickens do well enough scratching it around, but I still run a leaf rake across it from time to time for peace of mind). No mud, no odor, no flies, etc.
Whenever I need to service the DLM in the coop, I simply move it into the run since it's the same material - or, if it's began to compost, I'll add it to a pile. Same with the run bedding - I'll sift the compost out of it and leave larger wood chips to continue the process.