As for the issue of one tank or two, I can only state from experience that you will have to dump gray water more often than the black water, and generally speaking running gray water down AFTER you are done dumping the black helps to clean out the dump hose...
For the piping, the toilet doesn't have to go directly over the tank, it's just easier to plum them that way, and it makes checking to see if the tank is full much easier, open the toilet valve and shine a flashlight down there and see what the level is. I've got a friend with a Keystone Montana 5th wheel, his toilet is piped at angles to the tanks.
My own bus is the same way, the tanks are forward of the toilet, I just ran the pipes with a decent incline (actually decline) to the tank.
First image is a bit blurry... but it shows the run from the toilet flange down and forward...
And the next one shows the pipe going down through the cargo deck floor to the tank... note the 1.5" pipe poking up, that is for the vent stack...
I used slip grommets in the tank, made fitting the pipe to the tank extremely simple.
There are many sources for tanks, but the best deal I found for them was on ebay from, Tri-State Rock Your World
seller is where i go mine from, he's got 36 gal tanks for $50 and also sells the slip grommets... He's not the quickest shipper on ebay, but he comes through!!
For other RV specific things, there is another dealer and though they have almost the same name they are totally different sellers. Tri-State Surplus
has a lot of great deals, she is a fast shipper too. I have bought from this seller over a dozen times!!