If you keep the bioballs you can clean them out by swishing them around in a 5 gal bucket with tank water. Depending on the aquarium (really in most home aquarium applications) it may be beneficial to get rid of them altogether.
Waterchanges will be the best thing to reduce the nitrate level, than altering your filtration/circulation will be the best thing to keep them down. Increased protein skimming, better water circulation, refugiums, and deep sand beds can all be used to help keep nitrates down.