I did exactly what you're going to do last fall and early this spring. When I encountered a little bump that threw things off, I'd just flatten it out. In the case of little holes, I fill them in. Now I want to be clear that I'm refering to bumps and dips that can be leveled with one (1) shovel full of soil. Anything bigger than that and I try to go around it if I can. I always go on the high side of the abnormality, because I can dig the swale deeper to accommodate the change. It pretty easy to make little adjustments as you go along. Once it fills with
water the first time, you'll know where to make changes. The bottom being level is what's critical to prevent puddles and islands. The
berm can vary quite a bit in my
experience. The MOST IMPORTANT thing is that the sill is perfectly level and able to accommodate the maximum flow without blowing out.
Don't be afraid to get out there and do some digging. Make mistakes and then fix them. Experience is the best way to learn this particular skill. Just keep trying until it's right.
Best luck to you