The way I learned to set intonation is pretty easy... but I'm no expert. As for neck adjustments, I just eyeball it until I get the action I want without fret buzz. When adjusting the neck (truss rod), I do it in about quarter-turn intervals.
Anyway, to set intonation, plug your guitar into a tuner (chromatic would probably be best) and tune it. Next, hit the 12th fret harmonic on the top string and then fret the note at the 12th. If the harmonic is sharper than the fretted note you adjust the bridge saddle towards the nut (I can never remember the direction, it could be towards the bridge-- if you mess with it for a couple minutes, you'll figure it out). If the harmonic is flatter than the fretted note, you adjust the saddle the opposite direction. Keep adjusting until both the fretted note and harmonic are in tune.
Just do this for each string. I usually will repeat the process because you will probably have to completely re-tune your git after doing this to all strings.
Hope this makes sense.
Cheers!