Yeah the basic major scale pattern on the guitar is.

Major scale Box (R = root: i = index finger, m = middle, r = ring, p = pinky)

e|-X-|-R-|---|-X-|---|
b|---|-X-|---|-X-|---|
g|-X-|---|-X-|-X-|---|
d|-X-|---|-X-|-R-|---|
a|-X-|-X-|---|-X-|---|
e|---|-R-|---|-X-|---|
i m r p


This is only one of a many ways to play this scale, but you'll see alot of quick passages are boxed in a similar way. So if you can master the box fashion it won't be hard to get those faster licks. The difference between what you had and what I wrote above is instead of stretching for the 5th fret, I just dropped it down a string. So your version of the F major scale (1-3-5), could be played...


d-----------0-2-3--etc.
a-----0-1-3--------
e-1-3--------------
i r i r m r or
m p m p r p


The 5th fret on E is the same note as open A.

This is the easier way and most common. Easy is not always right, there will be times when you have to stretch (Van Halen's tapping solo on "hot for teacher" is an example of having to stretch). If the book you're learning from says to practice it that way, you should. There's probably a good reason, but the box position you should definitely master and you'll definitely be faster with it. Alot of really fast runs use it because you don't need to move the hand up or down the fretboard, thus less loss of speed.