I am running new a/c, heating ducting, I need help with duct size

Without knowing much  else about your system, I would say that in general terms multiple 6" square ducts are moving more air than a single 8" square, obviously, and having individual ducts into rooms will enable zoning (i.e. individual climate control of rooms) which is a very nice feature. So, to say nothing of the fact that with more ductwork you will have more duct sealing to worry about and less space for everything else, I would say it's great to have individual 6" ducts into rooms is better than one 8" with branches.

Even though I think your 8" is actually 8"x14" (as needed to move aprox. 1000 to 1200 cfm for the 3 ton unit),  two 6x6 will still move almost the same amount of air and will allow for individual climate control should you need it now or in the future.