Phi angle, is angle in the XY plane, phi=0 is the positive x-axis itself. thata angle is angle between Z-axis and the "measuring" point.
Elevation angle = 90-theta
If you want to plot the radiation pattern in the XZ plane, you need to select 2D pattern and select elevation. This means IE3D will calculate the radiation pattern under varying elevation. To define the azimuth to get the XZ plane, you select Phi=0. To get the YZ plane, you select elevation pattern and make phi=90.
To get a pattern in the XY plane, you need to select 2D pattern, select azimuth and check the elevation angle (that should be zero for XY plane, so theta=90). Note that azimuth patterns under low elevation depends strongly on conductivity of the IE3D ground plane.
If your actual antenna has finite ground plane and you use IE3D with infinite ground plane, plotting an azimuth pattern under zero elevation will not give you useful information.