How does matter "know" where it is?

Question

Imagine there are only two rocks in the universe (and an omnipotent experimenter). The rocks are thrown towards each other from far appart. They can be on a collision course, or pass each other, depending on their relative motion. But how do they know? 

If there were an aether, or some spatiotemporal substrate through which matter evolved, then I can imagine how the rocks would "know" that they were colliding or not: they would collide if they were to compete for the same part of this substrate. 

If there is not aether, I can imagine our rocks knowing whether they are about to collide or not, only if they exchanged information (through light or similar stuff). 

I am trying to imagine how spacetime could be emergent (maybe that's the error), and I need constant exchange of information between stuff for it to know where it is relative to the rest... I know my question will appear naïve to most, but I am obsessed by this question and I would appreciate any reference to relevent material on that subject. 

(Precision: One may answer "It is the electromagnetic force that will make the atoms of each rock stop the rocks from continuing on their trajectory." I know that, my worry is something else. It's how stuf knows where it is, if there is no spatial substrate. Maybe physicists use the various fields they work with as essentially playing the role of the thing that is telling stuff where it is relative to the rest ?)