Most likely, the six patterns you are referring to are patterns for sentences of a single clause.
But the sentences you are asking about are combinations of two clauses, one embedded in another.
I saw shows the subject and verb of the main clause. (The same analysis applies to
I heard.) The words that follow this subject and verb combination form a clause which acts as the (direct) object of
saw (or
heard).
I saw (something). I saw (him run / him running).
I heard (something). I heard (him whisper).
The embedded clauses also consist of a subject and verb:
him run; him running; him whisper; ...
It is just a characteristic of certain verbs (such as verbs of perception like
see and
hear) that the object clause has a subject in the objective case (
him instead of
he) and the verb in the object clause can be the bare infinitive or the gerund.
CJ