Setting up
If you want to set up your guitar differently to how it is already then what follows is a guide to the steps to take.

The Action
The most important factor in the playing feel of any guitar is the distance between the strings and the neck. This string height is known as the 'Action' of the guitar.
Each of the strings fits across an adjustable metal 'saddle' at the bridge. The saddles are adjustable up and down for the string height and backwards or forwards for the string's 'intonation.'
To change the action you must first loosen the strings, then use the small allen key provided to change the string height by inserting it into the allen screws on each side of the saddle. Turning clockwise will raise the saddle or anti clockwise will lower it.
Make only slight adjustments, then re-tune the strings and play to ensure that they do not catch on any of the frets or pickups. If they catch on the frets then the action is too low and you will need to raise the saddles. If the strings catch on the pickups, then you can adjust the height of each pickup individually.

Pick-up height adjustment
You can adjust the height of the pick-ups using the screws directly alongside the top and bottom of each individual pick up.
Press down all the strings at the last fret and ensure clearance of all the strings above the pole pieces of all the pick ups. The bass strings should be slightly further away than the treble strings. Turn clockwise to raise the pickup and anti clockwise to lower. Experiment to find the exact position which gives the best sound.

Intonation
Although the intonation of the guitar should already be set, adjusting the height of the strings can cause enough variation for the guitar to need the intonation re-setting.
Plug your guitar into the guitar tuner and tune the strings to correct pitch. Now check the tuning of each string individually at the 12th fret. If higher in pitch (sharp), lengthen the string by turning the screw at the back of the bridge behind the saddle of that particular string, moving it backwards. If lower than pitch (flat), shorten the string by turning the screw to make the string shorter, moving he saddle forwards. Once set up in this way the guitar should be perfectly in tune with itself all the way up the neck.

Finally.....
When you first start playing your guitar, it may slip out of tune initially. After tuning play for a few minutes to let all the strings settle, then retune and enjoy!!

All the information supplied here is as a guide only as there are so many different ways of setting up a guitar. If you get into any difficulty you can always contact your dealer who should be able to help you.