I am having a lot of trouble understanding the "magic" side of this game, in particular what to do with "spell points" the game lets me put 2 into "prayer" but wont store them and won't let me put them anywhere else. I chose "Brawling" as my magic type

Maybe this will help:

Lords of the Fallen Wiki

There may be other good websites for information too.

It states there are 4 spells connected with brawling, what and where are these spells and how do I give them points

Here is some more information that I found:

Brawling spells

And this should help as well:

Lords of the Fallen Level Up Guide