This is a question that comes up at least every other time that I set up an acoustic guitar.
WHAT IS INTONATION?
I made a little sketch of a compensated saddle and now I will explain the physics. Lets assume your scale length is 25," the vibrating string on the high 'E' should measure at 25 and 3/32". The additional length is added because when you push down on the string, it's no longer a straight line, so we compensate for that by moving the saddle back 3/32". The 'B' string diameter increases by .004 to .005 of an inch (depending on the chosen string gauge). This string has less elasticity, so when it's pressed it needs more length to achieve the desired pitch. The 'G' string diameter moves up .007 to .008" but it's a wound string so it's tension is only determined by it's core which is similar to the high 'E' string. The remaining strings are also wound and the compensated saddle slowly moves back to accommodate the thicker strings. Playing in tune becomes paramount as your ear develops and intonation will become more important on your way to perfect pitch. I hope this helps, till next time. Al