Spoiler:
There are defintley two time lines happening with Delores, and Bernard/Arnold...
The times that she goes and visits Arnold in the old lab beneath the church - she is talking to Arnold
The times that she is in the new labs - she is talking to Bernard.
The whole time I was waiting with anticipation trying to imagine what Arnold looked like, and the whole time they were showing us who he was, but it was always out of context, and made me wonder how the hosts would leave in the middle of the night to meet with Bernard(Arnold)
Delores also shows the two different time lines when she is with the Man in Black, and with William, who is one name calling away from being the same person (is the same person)
Most if not all the other characters depending on where you see them Delores/men in black, or Delores/William each follow the chronological flow, with the exception of a few, of whom the Man in Black makes note of through out each encounter.
Whats bugging me is if the Man In Black met the real Arnold or not, and now that Bernard is dead if they will just leave that for us to make our own assumptions...