Hello and welcome to the forum. You did not ask but you really should know the species, I am almost positive that it is a Chinese Pepper or Zanthoxylum.
Compare it against this clearer picture.
the booklet that came with it didnt give me too much information.
No surprise there, I would not put much stock in the booklet they are notorious for trying to oversimplify bonsai care and are often just plain wrong.
How much should you actually water the bonsai tree?
Until it is saturated. Watering is not about quantity but frequency. Water thoroughly each time then wait until it needs it again.
I know you're supposed to do it once every other day,
If this bit of information came from the booklet it is good example of bad information. Water as required not on a schedule. It may indeed be every other day but it may not. It may require watering every day or every third or fourth day. Let the soil itself guide you not the calendar.
I've been spraying the leaves each day too, shall I just continue doing this?
Sure wont hurt.
As for the feed, I mixed 1 litre of boiled cold water with 5ml of liquid based fertiliser, but wasnt sure exactly how much to feed it? Any measurements at all?
Assuming you mixed it at the correct ratio the advice for watering pretty much holds true here as well. Fertilize at the ratios and frequency suggested on the packaging. When you do fertilize you should water as usual first then a few minutes later apply the fertilizer as you would when watering. Make sure you apply it evenly and then stop when it begins to run out of the drain hole.
And finally for now :p what about pruning, when you prune a branch, do you take it right back to the trunk, or just leave a bit sticking out?
That's a little trickier. There's pinching and there's pruning for shape. If you want a branch gone then cut it back to the trunk or parent branch.
Pinching is more to maintain or refine shape. I am unsure as to how this particular species responds. There does not seem to be a lot of information on this one available. You could shorten one shoot and see where it puts out new growth. Then you will have a better idea of how to proceed in the future.
Does anyone out there grow this species?
BTW, what kind of light are you providing for it? Inside, outside? Window, supplemental lighting of some sort? If so what type?