I would think that on a 90G you would be safe running all four bulbs on the tank the whole time. You only have 2.4 wpg. I would probably be safe running both sets of light on mine also but I think it is a little safer running less light. Once things settle in I will probably run the burst for a bit longer. I don't think that running less light will help your colors much. Chances are you would have better colors with a bit more light as long as you keep up with your fertilizers and CO2. The down side is your plants grow faster and it might be hard to keep up with the trimmings depending on the types of plants you are keeping.
I wouldn't mind having my plants grow faster... more stems to sell=more cash to fuel my aquarium addiction. Can't complain!
And yeah, i'm planning on bumping up the lighting with two more 54 watt bulbs once i can afford to purchase another retrofit from catalina aquarium.
Anyway, do you have any plans of what fish you're going to put in your awesome tank yet? I think some congos would look pretty sweet.