There's really no other way to do it than by ear.
Here's how I do it. Start with the bridge pickup (this is always the one closest to the strings, so you'll see the logic in a minute). With the guitar plugged in and set to clean, strum the open strings and pick them one by one - every string should ring out at the same volume. If they are uneven, raise the quiet side by quarter turns of the mounting screw until you get an even response. Once this is done you can raise or lower the pickup without messing up the volume balance - if you raise one side one full turn of the screw, jut raise the other side the same and you'll keep the balance.
Now, either raise or lower the bridge pickup. Raising it increases the output as it gets closer to the strings, but too close and you'll start noticing strange effects, muddy tone and poor intonation. Raise it just high enough to get maximum output before the wirdness begins - the 'sweet spot'.
The neck pickup will always be lower than the bridge pickup so no need to do it like that. Balance the string volume as before and raise or lower it so that it matches the output level of the bridge pickup.
There are no hard, fast rules about all this. Some like the pickups a little lower than the sweet spot because they feel it gives a more open, airy tone (at the cost of a little sustain). Others like the bridge to be higher output than the neck so that they can flick from one to the other and get a little boost. But the above should give you a decent starting point.
If you're not confident about doing this, don't do it. If your guitar has never been set up properly by a professional tech, then this is the ideal excuse to get it done. You'll be amazed at the difference.
