In the book they go in length about the integration process. And how this is currently Ethan's 3rd integration attempt. Kate's third (if I remember right), etc... Also in the book Ethan's wife and kid never went on that trip and had their oil line cut. Pilcher went to their house the night she had her final 'going away' for Ethan and offered her the choice of going to Wayward Pines to rejoin Ethan or never seeing him again. She declined, more or less, and Pilcher ended up kidnapping her.
Then she woke up 5-7 years prior to Ethan waking up. Pilcher wanted her assimilated prior to Ethan waking up to make his integration easier. In the book the kid is only 5 when Ethan disappears and is then 12 once he wakes up in Pines. So those little changes they incorporated in the show kind of throw off a couple of things. Based on what we've seen in the show so far a long with what we know from the book, I'd say that her and Ben driving to Pines to find Ethan actually happened, Pope actually cut their lines, and they got put in cryo stasis. He basically explains in the book how all the non-volunteers visited Pines and were met with some accident which put them in stasis.
The last episode covered a lot of this but not in so much detail (and not as well). The Pilcher flashbacks in the book were better. The relationship with Pam and her origins is different. The Pope stuff I think was more flushed out in the show.
Their memories aren'timplantsnecessarily, but they definitely talk about some memory manipulation. Like in the book Ethan was a POW and tortured extensively in Iraq. Pilcher talks about how they purposefully activated those memories so that Pope could use them against him.
I need to start book 3 before the show ends. Amazon has this for rent on Prime for Kindle btw, so you don't even have to buy it. Just check it out for two weeks or whatever. The books are a super easy and quick read and not half bad.