I house mine 'together' so to speak. They share the same run space...and I have an 'up & down' coop. Bottom level was for ducks, top level was for chickens. However, the ducks moved themselves to one of my other chicken coops (the only one that isn't raised off the ground), and now sleep with the chickens. They sleep under the nest boxes and/or under the ramp, so don't get pooped on...but I have one duck that will sometimes climb the ramp and sleep with the chickens (I have a slightly sloped 'roof' to the nest boxes that acts as a poop board under 1 of the roosts). This 1 sweetie (duck) likes to sleep there at times. I also have 2 ducks that will hop into the raised nest boxes to lay sometimes. They do very well together! The ducks keep the roosters in line (well....control the roosters), so there is no issue there.
A couple of things to consider, though:
IF you have a drake, make sure you have enough female ducks for him, though. A duck's anatomy is different than chickens, and he (drake) can hurt hens if he tries to mate with them.....which he will only do if he doesn't have enough duckie females. (1 to 4 per drake, depending on the breed)
Water. As you know, ducks love to play with and make a mess of water. This means that sometimes they 'play' all the water out of the dish so there is none left to drink! (In the winter when the ducks just get a small 'duck bath' with added deep water dishes...in the summer I have a larger pool & nipple waterers - which the ducks can't mess up!) My solution is to raise one rubber water dish high enough so the ducks can't reach it, and place a roost next to it so the chickens can hop up and drink CLEAN water. Though they usually prefer the dirty duck water,,,
Other than these 2 things to consider (well, plus the fact that ducks make a mess with the water, and chickens don't like damp, so it means either a designated area for waterers with plenty of other dry space in the run, and/or lots of frequent changing of bedding.) Note that I NEVER put water in the coop, regardless, but you absolutely can't with ducks.