Doppelganger Cooper (Kyle MacLachlan) and the weird family in the woods spend several scenes talking about Bill Hastings's secretary (who is probably "Betty the assistant" we hear Bill mention in his interrogation). In fact, it sounds like this Betty person has some information that Evil Cooper is dying to get his hands on.
"This information seems pretty important to you . . . she's Hastings' secretary. She knows what he knows," says Ray Monroe (George Griffith) to Evil Cooper at one point. Cooper also disposes of Phyllis after she leaves the jail, telling her she "did good . . . You follow human nature perfectly. This is George's gun," he says, then he shoots her in the head with it, presumably framing George for her murder.
What does all this mean? Well, in regard to the secretary and what she knows and what Bill knows, we are still in the dark. But it seems likely that Evil Cooper and the weird family conspired to commit these murders and got Phyllis to help them by revealing Bill's affair(s) to her. Then Evil Coop kills Phyllis to tie up a loose end.
