Evil Lennox was with Emma. Emma suspected it after being in bed with him, so she said that thing about "going back to Fiji" because if he said what he said, then she'd know that he was a fake, and confirm her suspicions.
Evil Lennox blew up Emma, and then disappeared until the end of the episode, where he got shot.
Good Lennox was the one that was "freed" by Syd, and was in CIA custody the whole time.
The DNA process is a complete match, except for a small defect in the eye, to be able to tell them apart.
Good Francie must have been kidnapped about a month before, and been used for the cloning thing. The clonee, it doesn't take a long time. But they would have to have brainwashed her to get her to forget it. I think that's one of those details we're supposed to not think about too much.
Ethan Hawke won't be back soon, but next week we get Christian Slater instead.