I don't see any problem with that. I do that often with my ducklings. I watch how they respond to respond to the heat and decide to add extra or remove it. In the summer the heat source is usually not as needed, depending on where you live. At night, you can heat just one side of the brooder and...
Also you will want to keep an eye on the Pekin. They tend to overheat easily. You may need to fully turn off the brooder heat early anyway. I can't say for Muscovy, since I haven't raised them from ducklings. They will let you know if they are too hot or too cold. They start panting a lot when...
Watery poop in Pekins is pretty normal in my experiences. Ducks when they drink a lot more water can have more watery poop. It will range in consistency. I found my Muscovy to have far more solid droppings than my other breeds. I wouldn't worry too much unless you notice other signs like not...