I would probably start Hayne over Thomas since he brings some scoring. that way you have some rebounding off the bench. I try to think about what 5 players will be on the court. Your starting center had some rebounding, so Hayne can be some offense in the front line. Thomas will get a lot of PT off the bench anyway.
Unfortunately you can switch defense IQs that easy. I would go with man-to-man since you have better IQ there overall. It may expose you to some vulnerability but I still think it's better than going zone. I play a zone at my DIII team but it seems to be an uphill battle. M2M is better in most people's opinions and I think I agree. Either way, your team has some work and will take a few seasons to get better. I'd be happy to help advise if you have other questions - just site mail me.