With any breeder box, even the manufactured ones, I flush with tank water daily/twice a day if I keep fry in them. They can never have enough flow through them in my opinion, even a net breeder. It gets covered in some biofilm and small particles from the water, and eventually provides no flow at all.
Go with what you have, cover the bottom with a thin layer of gravel/sand, water will still go through but the fry won't escape. Add some cuttings from live plants to provide cover and additional micro fauna the fry can nibble on. And flush tank water slowly each day, morning and evening(or whenever). The left over food can be removed with a syringe. That's why I prefer sand, because the uneaten food becomes like fluff on top of it, easy to see and suck up.