Hi Michelle,
When I used to breed clownfish I kept the broodstock system separate from the larvae system. Typically they recommend this because you have to inundate the babies with so much food that it is easy to quickly degrade your water quality in your larger system and requiring more and larger water changes. I used water from the broodstock system to make small, regular water changes in the larvae system and then replaced the water in the larger system. I did have friends that had large systems like what you are wanting to do. They used either small breeder nets that hang on the tank wall or constructed a shallow tank in-line with the large system and had small plastic (~1 - 2.5gal) tanks with numerous holes drilled in them and fine mesh over the holes so you had some slight water movement through the tanks. As long as you can control the water flow so the babies aren't pinned to the walls or the food doesn't stick around for very long you should be ok. Another thing to consider though (for at least the clowns) is that initially they need a very dark tank with only minimal light from above as they have difficulties locating food in brightly lite environments. As they get older, you can gradually increase the amount of light they receive because their eyesight gets better as does their hunting abilities. Good luck, it is a lot of fun!
Jamison