You don't need to pray by pressing the button over and over, you can hold the key down and allow your keyboards key-repeat do the rest.
You 'pray up' your weapon everytime the 'you pray' text appears, the problem with the 'pressed it once' confision I think is around the fact if you press the key once, your gani keeps praying indefinately.
Here's the rule of thumb: deplete your grace, and if it's going up fast you are praying can blessing/gaining resistances etc.
If it is going up slowly, then whatever is happening is not a repeated praying.
I agree about the newbie guide.
P.S: I have noticed when I bless 5 weapons in a row, I can't get the next one to bless in any real timely manner, so you may also tick the gods off or something if you get too demanding.