Welcome to BYC!
By "taking over" the nest boxes and mention of him leaving waste in them I wonder if what you are experiencing is him sleeping in the nest boxes vs. making the sort of exploratory visits that can encourage hens to do the same. Can you tell us a bit about your coop setup or, better yet, post some photos? Often there are factors involved in the coop interior that make the nest boxes attractive that have nothing to do with their intended use as a place to lay eggs.
What breed(s) are your birds? If you are not sure, you can post photos of them too and we will help you ID them. The breed(s) are a point to consider as different breeds have different maturation rates and that factors into the expected point of lay for females. Seeing the birds will also allow us to help you see possible indicators of how mature the females are and whether they are showing phyiscal signs of being close to production or not. When in thh spring did the females hatch? "Spring" is a pretty broad term with the potential to have a +/- of 13 weeks or more in the actual age of the birds.
While gender balance can be an issues (as mentioned above) it is not always a problem as there are many factors that play into whether your numbers may or may not work - and, actually, many breeders use "trios" (2 female/1 male) for breeding groups. This would go back to assessing the overall housing situation, the breeds in question, the temperament of the individual birds, etc. Are you seeing signs of distress or overbreeding such as feather loss in the females, a stressed atmosphere, etc?