Is there a standered specing for furnace vent pipes?
The furnace intake and exhaust can run side by side as they will terminate next to each other. As for the termination, it depends on what the manufacturer allows. Could be a concentric, a bay vent or just two pipes. The holes will also depend on what size venting you use, most use 2", but higher btuh furnaces require larger pipes. You'll have to do a heat loss to figure out the sizing of your furnace. Also, you'll have to follow the manufacturer's specs of both the water heater and the furnace as to the clearance issues of the vent terminations, as well as all applicable codes (eg. The intake must be 10' from your gas meter's regulator). And finally, I should add that it is because of all of these issues and more that gas appliances must be installed by a qualified person. I know this is a diy site, but I see so many code violations and just simply stupid things done with gas on a day to day basis that I can't stress enough to either do your homework and research diligently, or hire a pro.