This is the tricky thing about reading music for guitar, but there is a system / method.

There are different positions you can choose to cover the range of the music you're reading. A lot of it depends on what the highest note is.

In my experience there are roughly 3 positions, within which you can generally cover all the notes you need:

Open through 5th

5th through 8th

9th through...

Once you get into that upper territory on the high E string, there will be tons of ledger lines. So it will hopefully be notated instead with the 8va symbol, meaning you can write it all down an octave so it's easier to read.

This requires learning all the notes in each range, and also connecting the ranges. As Steve Vai said, learn each note on the fretboard "cold."

I often recommend the Mel Bay Method books for basic reading, to get you started. Most of anything you see on the treble clef (minus upper ledger lines) can all be played in Open through 5th.

-Carl.