The good thing is that since your birds are young, you won't need as much space right away. However, are your two groups integrated now? More space is better for integration.
One problem with having the nest boxes in the run is that you either need to leave the pop door open all the time, get an automatic door, or make sure you always get up early enough to let them out so they have access to the nest boxes. Also, the eggs are more likely to freeze in winter. If your run is not secure, eggs in outside nest boxes are more vulnerable to predators like crows. You'll need to check for eggs that might be layed later in the day because eggs left in an unsecured run overnight will disappear.
