This question is going into the minutiae of rules. A spell scar is prepared "using the rules for scribing scrolls." You may scribe "a scroll of any spell that you know." Therefore you must know a spell to make a spell scar of it. In a pathfinder context, what does the word know mean?
"A wizard may know any number of spells. He must choose and prepare his spells ahead of time by getting 8 hours of sleep and spending 1 hour studying his spellbook. While studying, the wizard decides which spells to prepare."
This implies that wizards know the spells in their spellbook.
The knowledge pool ability does not say that you know the spells. It merely says that you can prepare them. RAW I do not think you can create a spell scar of those spells.
If you could tattoo yourself with any spell for the cost of 1 knowledge point and a little gold, your spell book would be nearly pointless. You would be able to build a secondary more powerful spell book on your skin, without being required to search out the spell first.
EDIT: Paizo lead designer Jason Buhlman said about the knowledge pool, "The issue I am seeing here is the ability to prepare a spell using this class feature and then copy it into a spellbook. The intent was to allow you to simply prepare and cast a spell by using up some of your arcane pool."
The other answer differs from mine because we are reading an ambiguous sentence in two different ways. I believe that the only way a spell counts as being in your spellbook, is for the purpose of preparing the spell for that day. This seems to be the developer intent.