I'd use an epoxy type wood filler since you're painting, not staining. Read the can of poly carefully, not all can be used over paint.

As an aside, how are you attaching these new boards to the existing table top? You need to consider wood movement otherwise the boards can crack or come apart at the seams.

A second warning on the need or desire to put polyurethane over paint. Enamel paint is essentially varnish with pigment. Why would adding varnish without pigment over the top do anything more for you? You risk it yellowing or peeling off. If you are really looking for a poly-like finish, get some oil-based floor and porch enamel.

Poly is not the be-all end-all of wood finishes, despite the way it's marketed.

Just avoid low-end latex paint.