Wet out the covering layers and cover the layup with plastic wrap (epoxy won't stick to it).
The wood pieces press the flanges to make it nice and flat.
If I were going to make several parts like this, I'd probably cut a piece of plywood
into a "U" shape for this step, but for a one-off, just a couple of pieces of wood worked fine.
Then put some weight on the wood parts to compress the flange a bit while it cures.