Hey im in no way new to playing bass or guitar for that matter. but im learning more about theory. How do you apply scales to a song? Because you dont just play the entire C major scale for example. You dont play every single note in ascending order. Im just trying to understand it. Thanks
Do you mean as a solo or lead?
Normally it depends on what kind of feeling you want out of it. Watch melodic control (http://video.google.com/videoplay?docid=5777562536751428345), it will tell you what you want to know.

Alot of people just play whatever feels "right" in the scale. Others will just play random notes and steal licks that are in the same key.
[U]        | |                     [/U]
[U]        |/     .-.              [/U]
[U]       /|_     `-’       |      [/U]
[U]      //| \      |       |      [/U]
[U]     | \|_ |     |     .-|      [/U]
      *-|-*    (_)     `-’