For the pen, there needs to be a grade - about 2%, so that the water runs out of the pen and does not puddle.
Even on a flat area, what you can do is dig a shallow channel on one side, and rake the pen so that it has a little tiny bit of slope toward the channel. Aim the channel toward a garden bed. If there isn't one, I strongly suggest you make one. It does not have to be large.
I have the day pen on a 2% slope, with a channel to raised garden beds downslope. Works great.
For the base of the pen, I add some chopped straw every few weeks, and use a cultivator tool to turn it from time to time to keep it aerated.
Stink comes from a lack of air. If you provide some straw or dried leaves or chopped flax fiber, and some air, you should get a nice compost with a pleasant aroma.
I have thirteen ducks.