I agree with Tyler that leaving an area of wild forest would be good. You could harvest
wood from it, while also providing valuable
native habitat. One area that would be great for that would likely be the that nice wet area. You could actually leave as it is as a sort of wetland preserve...and then you don't have to worry about draining it! There are various edibles that do thrive in wet areas (serviceberries, and lots of other berries, though I don't know which ones grow in your area). Also the plants and soil in a wetland is really great for slowing the water seeping into the earth. This is great, because it naturally purifies the water as slowly filters through the ground and plants, and it helps add a lot of water to your
local aquifer.
I really like a lot of the design ideas that you and Tyler have going on here. You might also want a tiny herb garden/spiral right next to the house, perhaps in the front yard or even on your patio in pots. I really appreciate having my herbs close to the house so that I can run out there, often without shoes (if the herbs on my patio) to get herbs to cook with. If the plants are really far from the house, it's harder to want to be spontaneous and pick some extra herbs or leaves for a salad.
I also like Tyler's placement of the ducks by the pond, as they would thoroughly enjoy bathing and eating in there. And, if you don't have too many ducks for your pond, they shouldn't do too much damage to the pond's ecosystem. Another advantage to ducks is that you can herd them from place to place. So, if you have paddocks, you can herd them to a paddock (chickens don't herd, from what I've heard, and thus need to be moved around via
tractor or mobile coop). Ducks also respond well to song, and if you sing a song each time you
feed them, they'll soon come running to you whenever you sing that song, and they'll follow you as long as you're singing. This comes in handy because it's a lot easier to make a stationary duck house than a mobile one, especially if you want to pull it by hand and have more than 4 ducks. You could also house the ducks with the chickens if you have no drakes (male ducks), though drakes are nice as they allow you to not have to by more ducklings every few years, and they are also quiet (unlike roosters).
I hope that helps!