I had a 90 gal
fish only tank for several years and brown algae was my biggest problem. I'm about to get back into salt tanks and I'm intent on not stuggling with the brown stuff again. Here's what I've been hearing from this site and other sources:
Silicates are one of the primary things you want to reduce to keep brown algae down - use only RO
water to keep from reintroducing silicates into the tank. Use a good substrate that won't put silicates into your water. I was using Florida beach sand and apparently that was a really stupid thing to do. I've had people recommend crushed coral as a good non-silicate leaching substrate.
Also, most folks seem to agree that you're going to go through a short brown algae spell when you start up/cycle. That's what you're doing now, so I wouldn't get bent out of shape about it. If it persists after a couple of months, I'd get concerned.
Again, I'm passing on what I've heard/learned from others, so if any of this sounds out of whack to others, please feel free to correct.