One thing I've heard is that you want to "
plan a swale on grade" because it requires the least amount of moving of dirt.
Then there's reality and it sounds as if you're dealing with that, Gwen! Sooo...
If the bottom of the swale is level, the swale will fill with water to the same depth everywhere and that water will hopefully all sink into the ground rather than run off. If you have to have deeper/shallower areas due to obstacles, just be aware that the shallow spots won't get as much benefit.
If the top of the swale is level and on grade, if you have a *really* big storm, the water
should overflow everywhere along the edge like a "sheet". If the top is *not* level, whatever spot is low, in a big storm, all the water will exit from the low spot in a rush risking erosion. Depending on the type of storms expected, some people intentionally plan for that and treat that "low spot" with flat rocks and a place for that water to go that's safe and responsible.
At this point from your description, you need to see how it responds as is to small storms and try to picture what would happen if it was a large storm and just make sure you aren't going to flood yourself or your neighbor any worse than if you hadn't altered the yard at all.