The difference between bioballs and live rock is this... BOTH promote growth of nitrifying bacteria on their outer surfaces, while live rock also houses DEnitrifying bacteria deep inside it's porous structure under anaerobic conditions... in my case, the bioballs are in the area of the sump where the water overflows to and through the bioballs, then through prefilter sponges on it's way to the skimmer intake where I would estimate 75% gets skimmed and the remainder passes through a refugium area in the sump with a 5" gravel bed that would host the DEnitrifying bacteria. The skimmer effluent is directed through this area along with the refugium effluent, and back up into the system. I carefully planned the route of my water to have it run this way. It offers me redundancy in case my skimmer shuts down or gets clogged, and like I say... ZERO nitrates. As an extra measure, I run a Phosban reactor in the last water compartment just before the water is returned to the tank...
I must say it IS cramped... and it IS complicated... but that's just MY way... do whatever works best for you and your system. 
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135G Mixed Reef. Bullet 2, 25 gal refugium, 2 X250W MH + 4X 96W PC\'s, DIY Calcium Reactor, Coralife 1/6 HP Chiller, Phosban, Tunze, 2 closed loops & SQWD\'s, Seios, Coralife 4 stage RO/DI & a bunch of other expensive gadgets... I may never retire, but I'm gonnahavahelluvanaquarium!
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