This is a complex matter. One way to start is to clarify the meaning of present:
Cambridge
Present:
in a particular place
There were no children present
Now let us separate the various suggestions Newton asks us to consider:
Newton is suggesting that animals perceive things (=sights, sounds, smells, touch). He calls these the Sensible species of Things because each is sensible (=is sensed by animals).
He suggests that there is a place in the animals where the perception occurs. He calls this the Sensory.
The Sensible species (presumably originating from the eyes, ears etc) are carried to the Sensory by the nerves and brain.
He last suggests that the Sensory contains a sensitive Substance that detects the Sensible species when they arrive there.
The sensitive Substance is present (in that particular place, as defined above) in or at the Sensory (Newton uses the preposition “to” rather than our contemporary “in” or “at”).
Perception occurs when a Species of Thing (sights, sounds etc) is present (in that particular place) at the sensitive Substance.
The whole idea is presented as a rhetorical question. For example, if I say “is it not time to go?”, I really mean “it is time to go”?