Eyes with round, centered pupils are easy to get right if you're adding them to the mold cavity then shooting the bait.
If the pupils are oval or otherwise not round, they're more difficult to keep aligned because when you're adding them to the mold cavity, you're looking at the opaque rear of the eye. To help keep yourself straight, take note of how the point or apex of the pupil is oriented with the "grid" on the back of the eye, and use that grid on the back to gauge pupil alignment as you set the eye in place.