Protein skimmers remove waste from the water column before it is taken into the nitrate cycle. This is a pretty big advantage over a HOB
type filter which can become a nitrate trap as gunk can build up in them if not changed regularly.
As for your levels, do you mean nitrate and not nitrite? Also, water changes to manage parameters in your tank must be understood. If you nitrates are at 50, then a 50% water change would cut that number down to 25. So if numbers are high enough, it can take quite some work to get those numbers under control once they get out of hand.