"I see one knife, not two."
Translation:Vidím jeden nůž, ne dva.
You are contrasting the objects, jeden nůž vs. dva (nože). Hence they should both be final in their respective clause.
You could say: Jeden nůž vidím, ale dva nevidím. I see one knife but I don't see two. This contrasts the verbs so the verbs are final. They can also be both first.