What sefer discusses the details pertaining to the writing of Nevi'im and Megillos (i.e., how the paragraphs are broken up, where there are "special letters", etc.)?
Minchas Shay is a commentary on Tanach that focuses on the correct reading (both k'siv and k'ri), including such things as paragraph breaks. (I don't know for certain that he comments on every sefer or which, but I know he does on many.) He does leave some questions open, mentioning both sides, and even where he takes a side I don't know whether sof'rim follow his decisions — but he is considered an authoritative source.
Meschet sofrim which is part of the mesechot katanot in bavli. It was written during the timesvof the geonim.
I recommend listening to Rabbi Wieder's Intro to Bible shiurim on YUTorah.org.