The Assign->Element->GeoTrans… menu is used to assign the type of geometric transformation you want to use to transform the frame element displacement response from the global to the basic coordinate system and frame element forces from the basic back to the global coordinate system. The choices are Linear, PDelta, and Corrotational. Please look at the literature to see what the differences are if you are not familiar with these coordinate transformations.
The Assign->Element->Rotations… menu is used to define the local y-axis (and z-axis) of an element for 3D problems. You can always check the orientation of an element by displaying the local element axes. Once you have assigned the correct orientation of your frame elements in the model, make sure that the local y-axis and the local z-axis of the cross-section are consistent with your desired element orientation.