Well first off... there are more than just 5 scale "patterns"...there are tons of scales. Check out "The Guitar Grimoire" it's basically a compilation of every scale known to man. Learning the notes on the fretboard is helpful in learning scales becuase if you know certain scale patterns, and where the root notes are in those patterns... you can find the root and play the scale. But you can also go about it from the other direction. If you know the scales and the roots, you will know where all the notes are on the fretboard. I learned all the scales that I know basically by playing... I have the book that I suggested above as well.. and it helps me with finding unique scales when writing songs or challenging myself with new exercises using scales that I'm not familiar with.