Fine materials will tend to pack down and form a water-repellent crust, whereas the bark will not, so depending on the texture of your manure mix, you might want to scratch the manure in shallowly, (just enough to remove the soil/manure interface), then top with enough bark so that you can't see what's underneath. That is only for established plants, I wouldn't till-in raw bark as a soil amendment, but after a summer of exposure, it could be raked up and mixed with a little more manure for use as an amendment.
If the crowns are pulling themselves deeper, that's normal, daylilies tend to do that. It means your soil has a decent structure, or that you might have put a lot of organic matter in the bed at planting time, and it's breaking down. They should stop pulling themselves deeper at some point. (In hard soils, the crowns in big, older clumps can end up sitting above the soil.) Instead of adding native soil to compensate, use it as an opportunity to add more mulch, since it will be "lighter" and will also feed the soil. Burying the crowns too deep with dirt might decrease flowering eventually.
