Sounds like you're on the right track. I say do whatever works for you. Delbeek and Sprung's Reef Aquarium Volume 3 has some absolutely AWESOME information on running systems various ways... they have used a totally open minded approach and have delivered some of the best information to date in this book, with some of the articles coming from some familiar places we go to here on the internet.
I just removed 7 gallons of bioballs from my system... just to see if this will give me some headway on some hair algae I have been getting... 
Alkalinity is something that can be monitored and controlled from almost day one. I add more alkalinity than anything else to my system in one way or another.
It really doesn't matter which way you decide to go, as long as you create a balanced, stable system capable of housing the animals you want to keep.
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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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