For cleanliness for the chickens I'd keep them separate if I was starting again. Mine are allowed out to a huge grassed area for a couple hours each day while I clean their sheds and put down more sand then back in their run, so they don't do an awful lot of damage - and they don't seem to bother about my veg raised bed at all - or the strawberry bed (but there's not many berries there) I have two sheds - the two light Sussex go in one, the ex batts in the other, the mother duck sitting on an egg is in there too and the other three sleep out all night so I can't shut their pop hole!
To sum up, if I was startign again I'd have ducks and hens in separate runs, let them out for a time each day, possibly fence in the veg. But I'd still have them all - they are great fun and the eggs are great. I wouldn't eat them though - no meat on egg layers (I wouldn't eat my own animals anyway but happy to eat other folks ones! lol)
Does that help?