actually I may be wrong. I believe that the water heater must enter the chimney above the point where the furnace enters so you cannot go below the furnace entry point. very rare that your case happens but you should check your gas code or local requirments. where do you live and maybe one of our other guys can verify that point.
Yeah, my local code needs the water heater flue to connect above the furnace for sure. Quick details on the construction of my home: It's a 1950s split level with the chimney in the middle of the house. The "chimney" is actually a round b-vent pipe that was installed inside the original brick chimney about 5 years ago. The bottom 4 feet or so of this pipe is exposed in my mechanical room (I kept the brick chimney from the second floor through the roof because I like the classic look of the chimney and it's in keeping with the other homes in my neighborhood). The b-vent changes to 26-ga. c-vent at this point as the walls on this level are concrete and besides that there is well over 9" of clearance on all sides from anything considered combustible.
So my plan was this:
Furnace: The furnace will remain on the first floor, but because it's a split-level it will only be about 5 feet higher than the water heater. The 3" furnace flue connector enters a 5' to 6' horizontal of 6" pipe via one side of a 6" wye that is capped on the other side. The 6" pipe connects to the chimney via a tee on the very bottom of the chimney pipe, right above the cleanout.
Water heater: The water heater, although physically located below the furnace, will have a 6-foot vertical run of 3" connector that takes its entry point to the chimney about 12" above that of the furnace, and it will connect to the chimney at a 45-degree angle via a wye with a reducer.
I'm relatively sure this meets local code, NFPA 211, and will be safe. If I've missed anything please let me know.