It really depends on whether you want/need to keep the chooks in there or whether they'll be allowed to run around outside the coop/run.
One of my coops has a nest box lift-up "door" on the outside and it has the pop door and the people door inside the run.
Pros: you can leave the door open and clean everything without having to first confine the chooks if you don't want them out and about or without having to keep out any "brothers and sisters" of other animal types like an annoying dog who will be trying to jump in there/have a look around. Having said that, it might depend on your chooks as to whether they'll go out. My little girls don't free range and they never try to go out the run door, even if I leave it open, and if I open the egg door when they are on the nest box, they just sit there, they don't "make a run for it". My dog, on the other hand, is all "what are they doing?" if he's around when I open the egg door.
Cons: you have to carry the "stuff" through the run, both the dirty cleaned-out stuff, and the fresh bedding (although I can chuck that in through the nest box opening if I want to).
If I was designing a coop/run, I'd do it the way my chook house is but I wouldn't fix the nest boxes (they are screwed down), I'd use ones that are removable. Then I could rake out the bedding through the "egg door".
IF you live in an area with predators (I don't) I'd put the people door inside the run as an added line of security. I've heard about those racoons and I wouldn't want them opening the people door.