Why did Newt tell Thomas to “lay low”? How did they prepare for their plan?

Do you mean chapter 53?

Newt emerges from the Gathering to tell Thomas and Teresa that all of the Keepers have agreed to his plan. He is sure that convincing the Gladers will not be as easy. Some of them will stay.

Newt leaves the code to Teresa and Thomas. He tells Thomas he'd place him in charge of the whole operation but that might make the Gladers upset. He tells them to run the whole thing from the background and lay low.