A properly baffled large tank should be as stable as a pair of small tanks...but if not baffled properly, you'll potentially have twice the surge forces in rough weather. You won't be able to trim your boat by drawing fuel from one tank or the other. A large tank must be very securely fastened to the hull. It also means that with twice the weight it must be properly padded to prevent abrasion wear from inevitable vibration. Whichever way you go, be sure to pay a LOT of attention to the "padding" used to protect the tank. In general, many tanks would, I think, tend to be more expensive than a few larger ones.
The shape of a tank, low profile versus high, can affect stability to some extent, but in general it's minor since the tanks are usually low in the bilge anyway. Be sure that any tanks do NOT sit in bilge water as that is never helpful.
As Trojan noted, separate tanks are nice in case of potential contamination from a load of dirty fuel. In practice, I always end up adding fuel to all three of my tanks when I take on fuel, so I've concluded for me it's a minor issue. Related, if you ever lose a fuel line or connection, with multiple tanks and proper plumbing you can turn off the leaky line and get home on a good one.
Finally, depending on the trim of your vessel and cruise speed, you might choose to put a tank way forward and another aft to permit better load balancing fore and aft. A final consideration: Can you fit in a standard size, off the shelf, tank or tanks? That might be potentially less expensive if you can get the material you desire. And don't forget to ground water tanks and fills you add to your bonding system.
