The Big 3 is:
Typically, the alternator is grounded through it's chassis and then through the bolts that hold it to the engine. You could run a wire from those bolts to the engine to improve the ground, but I don't think you will gain much.
As far as the Battery to Alt + wire - Most sites recommend stacking it on top of the wire that is already there. You could remove the original wire and only run the new wire, but you need to be sure that the new wire can handle the original electrical and you added audio, and it makes it obvious that the car has been modified when you get to re-sale or take it in for service.
Hope This Helps!!!
2002 Ford Focus Sony CDX-GT410u Sony XT-100HD HD Tuner Stock speakers, no amp, no subs