I keep them "together", if by together you mean "in the same run". I have two, actually, both have hen houses which are extremely well ventilated, so the extra moisture from the ducks is not an issue. Can't get around the extra cleaning, however - ducks will very rapidly fill watering stations with mud. Requires constant upkeep.
In the original run, the ducks bed on the ground (because of course they do), and the hen house is raised 3' above that. Sides are all metal cloth on three sides of the house at the duck level, so its all ventilated - 8'x12', so 24 sq ft plus 36 sq ft plus 24 sq ft of ventilation. No issues with the chickens roosting 4-5' above them, with a floor between them. That's also where my primary nesting boxes are, they remain in constant use.
Biggest disadvantage is having to crawl under the raised hen house for duck eggs. Its not comfortable or sanitary. I've transitioned my ducks largely to the second run, with the goats.
There, the ducks nest n plastic milk crates 3-4" off the ground, and chickens perch on a shallow ladder system I built above the height of the top of the milk crates. Goats bed down on raised pallets on the other side. Much more easily managed (this will NOT work if you free feed your birds- Goats can get severe bloat, potentially requiring medical intervention, if they eat too much poultry feed.)
I've never seen, though I have heard it possible, a drake try to mount one of my pullets. You can see my flock in the signature below. There is currently one drake. I've had as many as three mature drakes, and rapidly culled them to keep the drake/hen ratio relatively low. FOr the hen's sake, as much as for the chickens. My birds free range on a good sized pasture, with a small man made pond, when they aren't in the run overnight - mostly the ducks and chickens self segregate into separate "flocks".
To answer your question? As soon as the ducks can run effectively on their own, you can start to integrate. Which is some period AFTER your quarantine is done. I assume you plan to quarantine at least three weeks at some distance as far from the existing flock's area as possible? By age 5 weeks, ducks should have plenty of size, and as much coordination as they are ever going to get, you could start "see and be seen" sooner, except for the quarantine period, with an expectation to fully integrate two weeks after the see and be seen begins.
The only time I've had problems with pekins and chickens together was in the reverse - I had a large brooder (now a grow out pen, roughly 4' x 13.5') and introduced hatchling chicks when I already had several week old pekin ducks. In the race for the food bowl, those much larger, very ungainly, ducks crushed one of the hatchling chicks - something I hadn't considered. Put up a temporary partition wall and raised them side by side from that point forward. Integrated when the chicks were about 6 weeks and had some size, had them moved out at 10 weeks. Most of those birds are still with me.
