Ok here is what I learned while cooking my live rock.

Weekly water changes is a must for the first 6 weeks. After that, every 2-3 weeks will work. You will want to do a 100% water change with fresh saltwater everytime. The point of cooking the liverock is to deplete the algea and other critters from the live rock from any nutrients (both in the water and hidden from light). Using water from your tank will only hinder the rock from truely cooking.

If you do notice Aptasia, you can pull that piece of rock out and nuke it with a lighter. Burn the heck out of it. The rock will be fine. It will only be covered by the bacteria again later. Try to remove as much of the Aptasia or Bubble algea during the cooking process. When you do the weekly water changes, you will want to set up 2 or 3 buckets of fresh saltwater to clean your rocks with. Pick up a new scrub brush and clean the rock with it. It will scrape off any algea or pests. Then you want to dunk and swish the rock in the buckets of water. This will help clean off the rock. Trust me it works. The water will turn black...even weeks into the process. Its amazing how much stuff falls off that rock.

Other than that, its just a time consuming process. 2 months minimum.