Too much sand

[mbssampley]

I just recently, 2 weeks ago, got my 29 gal biocube cycling. It's almost finished. Before I got started adding a few inverts to begin with, I wanted to take some sand out. I was told but an online company to use 80 lbs of substrate. As I didn't listen, I did add too much. Some of the substrate was dry and 40 lbs is live. How long before the bacteria has spread throughout the sand so I can take some out? Will it cause a mini cycle when I do? There is about an avg of 2.5 inches but would like an inch less. Seems like too much sand could cause problems, maybe? I didn't want a "deep sand bed". Should I turn the pump off when I remove substrate or will that hurt the bacteria to not have circulation / added O2. Not sure how to go about it. Also, I have a Tunze 9002 skimmer; when should I start it up? After I get inverts? Any help is appreciated.