What you're doing is fine but not necessary if you install a big three upgrade. By ensuring that you have a good bond between alternator, frame, battery and body you can ground to virtually any other point on the frame or body with no problems. That said, if you do what you're talking about and the alternator is still only bonded to the frame, battery and body with the small factory grounds, you won't have the current carrying capacity you think you do.
The idea with grounding is to get a complete bonded path, that's capable of carrying a high current, from your amplifier to the case of the alternator. How you accomplish that is of no consequence.
