Magic manuals unlock new Witchcraft spells or upgrades. You cannot learn most hexes without the matching manual, so pick up every one you find.
Check ruins, haunted sites, bandit camp chests and scouting tower chests. Witchcraft vendors sell them too.
Read the manual to unlock the spell or upgrade in the Witchcraft tree. Then spend skill points at a road shrine to learn it. Watch the time cost before you confirm.