Nitrates are always going to be a problem till you get established enough to have the proper amounts of bacteria to deal with it. There are many ways to deal with them though. Water changes are the most effective, but also the most work. There is dosing with sugar/vodka/vinegar, but you will want to do a lot of research on these becuase you need a good skimmer and really good turnover rate. There is adjusting your feeding, feed less or every other day. And then there is a really good protien skimmer to get rid of food and poop before it turn into nitrates. Also, i don't beleive your problem is from stirring the sandbed up, becuase every time i have stirred the sandbed up, i get ammonia spikes, which lead to nitrate spikes eventually. If you didn't see ammonia, i would say that its becuase of the CC. It famous for trapping stuff and letting it rot. Its hard for CUC's to get clean, and needs lots of vaccuuming to work. Just my .02 cents.