This is a list, by Chapter, of all the monsters for which you will need a Bestiary entry before undertaking the quests in any given chapter. You may or may not meet all of them, depending on the choices you make as the game unfolds, but with the Bestiary entry, you will be able to harvest all the possible skinnable items for any of the beasts you do encounter.
The easiest way to get these entries is to just read the book that contains the entries you need. If you are a cheapskate, then there is some added complexity to getting the entries you need with minimum cash outlay. If money is no object, just buy all the books you need. There is always a merchant selling books, no matter where you are (and buying the ones you have read).
Boss monsters do not require a pre-existing Bestiary entry to extract the special ingredients.
There is only one monster in the Prologue and it is a boss monster, the Frightener. This entry is given to you by Vesemir, no need to track it down, and depending on your choices during the Prologue, you may not even need to kill it. Your witcher associates may do it for you.
The boss monster is a hellhound, the Beast.
The boss monster is a golem.