Jim,
That is not easy to answer.
It depends on the type of wax, the buffing pad (foam or cloth), what type of pad, how you boat is prepped etc.
It is not a requirement that you use either method.
But I for the most part use the buffer to apply and remove the wax as I go along.
I normally have to come back for the touch ups with a 3M Microfibre cloth.
Disclaimer: I use commercial finishing products so my methods my be different from what you have.
Try it both ways and see what works the best.
After many years of compound and waxing boats I leave my options open and use waht ever method works best.