"Good question Cuzco. I can tell you that stuff is spread over a huge area probably due to the constant surf action and the actual sinking dynamics. Mother nature never ceases to amaze me."
I assumed that if they were found all in one spot they were probably in bags, that have rotted away. I don't think these would have been placed in with the shares the men had placed in the main treasure area on the ship. It was likely that they were kept aside in the things to be later sold, or for general supplies and maintenance of the ship.
From reports, the dynamics of the wreck would have strewn them about, but the general deposition seems to indicate they left the ship at a time prior to the breaking of the hull apart in a single unit, and have not moved. Draw a line across between the two parts of the hull, and choose a point farther over to the mass of the larger part of the hull that was found, or make the center of mass the group of cannons conglomerated together.
Then pinpoint the center of the manila scatter with a point. Now connect the two points with a line, and then extend it out past the point where the manilas were found. This may give you the vector of the storm and search area past your old points to be looked at for deck cannons that ripped free, and things thrown out of the hold during the rolling process.