cycle/protein skimmer ??

I'm starting a new 75 gallon tank (1 day old). I only have my saltwater and live sand in the tank for now. I had a good bit of large fragments, from who knows what, so I turned on my protein skimmer. I DONT plan to leave it on, but I wanted to make sure it was ok that I used it for a few hours. The tank it still very cloudy from the live sand, but I don't see anymore fragments. I have about a half a cup of brown waste from the skimmer... Including a small spider... Did I mess anything up by that initial filtering? Now that I'm nervous, should I dump the waste back in?