Hi Rowan, glad you like the game. I don't know why the manuals were left out of the game - I bought mine years ago & didn't get one & a friend of mine just bought the game & didn't get one. Not to worry - I'll help if I can.
Have you become a vampire yet? If not, you don't have any disciplines yet. "Disciplines" are just their word for "spells." Intelligence , wits, etc. are attributes that you can increase when you make levels. You'll need to have a minimum in some in order to learn some spells. You don't have to worry about "faith." I think it goes up automatically.
Where are you in the game? Save your holy water for the silver mines. You can use it against a big bad monster in there. To use a healing potion, right click on it . To use the holy water, pick it up & right click it on the enemy. You can't use the rats until you become a vampire. Then you can drink their blood!
If you're still human, you should start out with a sword. You might be able to get something better or some armor at the blacksmith's.