"Do you remember that boy?"
Translation:Pamatuješ se na toho chlapce?
It most often means you are old enough to remember the time when the dead boy lived years ago.
It is also possible to use it in the normal meaning, just less common. But the meaning about remembering the dead is the first that comes into my mind when hearing or reading it.
So I think "Toho chlapce pamatuješ?" is correct.
They are usually not interchangeable and you have to learn them together with the verb. "se" is technically accusative, while "si" is dative.
This particular verb works with both, just slightly differently:
"Pamatuji si toho kluka." (direct object, "I remember that boy")
"Pamatuji se na toho kluka." (needs "na", and it's a little closer to "I recall that boy").