I've got a plane with a glassed and primered center section and the wingtips will be covered with flat black Monokote. The center will be finished with flat black epoxy paint. Would it work better to cover the wing panels, then paint the center section afterward, or visa-versa?

....vice-versa.

If it were me, I would cover the wings, then paint. I would wager that the paint would stick to the monokote (and seal the edges in the bargain) better than the monokote would stick to the paint.

That's what I was thinking, it seems like I've bubbled the paint from ironing over it. OTOH, if the temp is just right, the Monokote should stick real good to the epoxy paint. I've never worked with flats before.

I would paint, then Monokote. That's the way I always do it. I've never had a problem with Monokote not sticking to a clean painted surface.

....yep. Mono-cote sticks to paint two to three times better than to just wood.

FBD.