For the horizontal axis, continuous adjustment tracking option, you can set the axis of rotation to whatever you want. For an east-west axis of rotation, enter an azimuth of zero degrees. For a north-south axis of rotation, enter an azimuth of 90 degrees. (The azimuth will actually switch between 90 and 270 degrees as the sun crosses overhead at solar noon, but HOMER will take care of that.) We intend to clarify this by giving an explicit choice between east-west and north-south orientation of the axis of rotation.
Note that when you are modeling any tracking system, the slope and azimuth appear in the time series outputs in the Simulation Results window. That gives you a chance to verify whether the tracking system is working as you expect.