gaRCField,
Yes, the rudder is used to keep a plane tracking straight through a loop or any manuever that has a portion of a loop as a compenent. Usually the wind is the cause of throwing the plane off of track in a loop, and the rudder is used to correct for this. If you plane is always not tracking straight then the setup of the plane is incorrect and needs to be fixed. It's not only the lateral balance that will affect it. The location of the CG can affect it as well. Also, if the plane isn't trimmed properly it can affect how the plane will track through a loop.

Ken