You cannot apply fortifying stones to a creature.
While it is true that there are creatures with hardness (see animated objects), those are no longer objects but construct creatures. The effect of the fortifying stone clearly applies to objects, not creatures.
So, while your suit of armor could possibly have more than one stone, the benefits would only apply while the suit of armor is an object. This benefit should disappear once it becomes a creature.
For instance, while a suit of plate mail should have at least 10 hardness due to the metal's inherent hardness, a medium-sized animated object only has hardness 5. While you could use the construction points to add the Metal property and increase it's hardness to 10, it has little effect on the creature's hit points. Armor has AC * 5 hit points, the creature is fixed at 36 hit points.
Considering how detailed the rules for creating animated objects are, I would expect at least a mention of using the fortifying stones to build constructs. Like happens to the Irespan Basalt shown on Magnimar, City of Monuments, which has the following properties when used to create constructs:
Physical Properties: Irespan basalt is as hard as iron, while retaining its other stony features for carving and building. It has hardness 10 and typically fetches a price of about 5 sp per pound. However, since few buyers are interested in stones of less than 1,ooo pounds, the Irespan bas alt trade is relatively limited to specialists capable of harvesting and transporting such heavy blocks.
Building Constructs: When a construct's materials consist entirely of Irespan stone, its Craft DC increases by +5, but the required Caster Level decreases by 1. In addition, stone constructs crafted from Irespan stone gain a +2 bonus to Strength and gain twice as many bonus hit points as normal from the construct type.
We might see more on this subject on the upcoming Construct Builder's Guidebook.
As for stacking fortifying stones, you could possibly add several stones to a single object, and a lot community members seem to allow the effects to stack. The only thing that puts me off is the text about working like temporary hit points, as we know that temporary hit points from the same source do not stack (like multiple castings of Aid). But, considering the cost of each stone (1,000 gp), I personally would allow them to stack on the same object.