Its a specialism in its own right, it requires 3d artists to be versed on the needs of 2D and 2D to know how to use the 3D correctly.

Fx guide is good for guides on areas of compositing and I would worry less about after effects and more about the principles of compositing.

C4D might be more straight forward for compositing into AE but the difference is neglegable if you know what your doing.

Youll need good match move in order to clean up and deal with your footage accurately, 3D artists need to do bodytracks of characters in order for them to interact correctly with CG elements, anything that will have shadows cast on them will need to be remodelled for shadow casts. This is most easily done with good set photography and measurements.

You will need to get to grips with how different secondaries mix to result in a beauty pass so you save alot of CG being re-rendered.

Also colour correction and matching blacks etc is essential to get CG art to blend with the plate.

FX guide has a very strong compositing information and case studies. The topic is rather vast to be honest so it might be worth doing some kind of formal training.