Sounds like the scope line of sight is above the line of trajectory. It's common to need to hold over at close range. There will be a point at further distance where the line of sight and the line of trajectory will intersect, that's your first zero. Further out, the trajectory will likely be above the line of sight and you'll need to hold under to hit the target. There will be a point where they intersect again, that's your second zero. After that you'll need to hold over to hit the target. Do a search for trajectory and line of sight and you should find a diagram that helps explain what's going on.
hope that made sense,
John