This is my first attempt at stringing one of my own basses so bear with me here...

How do I set the "intonation" so that the open E matches the E at 12th fret, open A matches 12th A, etc? Every time I try adjusting the bridge saddles one way or other and then retune string, the open string and 12th fret aren't both in tune(12th fret is sharp).
I have a Squier 4 string.

Any help for this idiot?

Compare the fretted note to the harmonic at the 12th fret. If the fretted note is sharp, move the bridge saddle back a little. If it's flat, move it forward. Use a tuner if you don't trust your ear.

Open and harmonic at the 12th should be exactly the same so either way is fine...if not better find a new bass :D . Like Imoh said you should move the saddle away from the bridge if it's sharp. Keep turning the screw clockwise until it's matched.

Strobe tuner or one heck of a set of ears.