The conversations Dolores is having with Bernard? Those are actually conversations Dolores is having with Arnold from 34-35 in the past. Those are scenes in which Arnold, grieving over the loss of his son and disillusioned from his grief, is setting the stage to have Dolores destroy Westworld from within, setting up "the maze" etc. Sometime after this, Arnold commits suicide, but not before uploading his virus into the park system.
The scenes with William and Logan are taking place four to five years after Arnold's death. Westworld is on the verge of bankruptcy, and the company William and Logan work for are on the verge of buying the park. The name of that company? Delos. Of course, this is also 30 years in the past, and leading to "the incident." I'm guessing this involves the eventual death of Logan (who hasn't yet died in this episode). Such a death, of course, would result in a major overhaul of Westworld, and, since Teddy is also a major exec, would prompt Delos buying and overseeing the company.
Thus, after the incident, storylines are readjusted and hosts are reprogrammed. The level of violence the hosts can inflict on guests are also toned down considerably; they can't physically harm the guests in any way (i.e. no punching and choke holds), and bullets which used to knock them down and leave bruises are much weaker. This is also when Ford creates Teddy as means for keeping Dolores on the farm, so that she doesn't break from her loop again.
Sometime in-between those 30 years, Ford also creates Bernard, an android duplicate of Arnold. He does this, in part, because he wants have some insight into Arnold's psyche so as to prevent another incident, but also because he misses his friend and co-founder. It's also an ideal way for Ford to spy on people within the company, especially Theresa.
The "present day" is where we see William as the Man in Black attempting to relocate the maze again. And it's also when the virus has been re-triggered, thanks to Ford's "reveries." Dolores is also starting to remember how she broke from her loop, has done so again, and is re-tracing her steps alone to locate the maze again, while also having flashbacks to the time spent with the younger William.