I don't want to spoil the show for anyone, but the reddit group dedicated to this show has figured out most of the answers.
Pretty obvious that it was outtie Helena in Season 2 Episode 1, pretending to be innie Helly. Irving forces himself to stay up all night with loud music and coffee so that his innie will fall asleep and his subconscious will filter through. Notice how Lumon have a very strict no sleeping policy, and Selvig is always trying to get Mark to eat and drink things that will make him sleep? Dylan's wife is obviously in a wheelchair, which is why we haven't seen her yet, and his innie always talks about his muscles. He gets them from lifting her in and out of bed.
The whole Cold Harbor thing is pretty obvious as well. The numbers correlate to the five Kier values, which is why the heavyset dude has "frolic" tattooed on his hand. Gemma was a burn victim, which means they froze her body and showed outtie Mark S another body for identification. Notice how Miss Hoang was a crossing guard? They want young people who died in accidents so they can bring their consciousness back to life by recreating their personalities through DNA - which is where the MDT come into play. The ultimate goal is to bring Kier back to life.
The goats back this clone theory up. If you'll remember in the first season, the state senator's wife has been severed so that she won't have to go through the pain of childbirth. That's why she smells funny and chews oddly, and has scars on her head - from where the goat horns have been removed.
Pay special attention to how they put things in the drawers before they go down the elevator, or back to their cars at the end of the day. I strongly suspect Irving is using his watch to communicate messages between his innie and outtie.
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