I forget the stock measurement for pickup clearance under the strings, but it's mostly a matter of preference. If the pickups are too high then you'll get notes that flatten out and sound dull due to electromagnetic pull from the pickups 'dragging' the strings as they vibrate. If the pickups are too low then you can experience and lack of clarity and sustain. Find what works for you, a lot of people around here keep our pickups pretty low because of the positive effects it has on the tone.
Another thing to mention is that if you turn the screws on either side of the pickup an unequal amount of times, you'll notice that either the treble will be louder than the bass strings, or vice versa. You can play around with this to help form your sound too, but most people suggest just balancing your pickups to be even.
Have fun setting up your guitar. Learning how to do it yourself is an awesome thing to do. Guitar care and maintenance is a great hobby.
