I would imagine it is quite varied. Junior Chaplains might start out working with Scouts. Net up, there will be Chaplains who are trusted enough to work with the Reserve Companies, maybe even on a single squad basis. Above that you might get those who are senior enough to be trusted with a Battle Company, working with the Captain, attatched to his Command Squad. Then you would have the Chaplains working with the 1st Co, bombastic and vengeful enough to inspire the Chapter's greatest heroes.
Whilst the number of Chaplains isn't big enough for one per squad, I would imagine that there are junior members of the Chaplaincy working under a Company Chaplain; you might even get non-Chaplain squad members who are able to perform something of the same function. Maybe they are just inspired by their service to the Emperor, maybe they are actively trying to get into the Chaplaincy, maybe they are in training.
I see the Chaplains, their ranks and their duties as being a complex mix of things. I would imagine that there are also Astartes who are being looked at as prospective Chaplains at all stages of their service.
Just note that all of what I've posted is purely what I think could be the case; I haven't got any particular fluff-justification for this.
GFP