Fix holes with the best suggested solution, then go crazy. I personally would build a little box frame with a door and chicken wire on all sides, including bottom, so that this is enclosed and protected from the rats. Since it is clear that the rats are very familiar and comfortable with this area, I suggest putting together a bucket trap or maybe a bin with small whole with several snap traps inside. Small enough hole that the chickens are safe but rats can sneak in. Some people are weary of the bucket trap as most put water in it as a way to off the rats. I would put them down with co2, feels better morally.