Depending on your guitar's construction, the bevel on top of the bridge may not be symmetrical. In some cases it may actually have some abrupt changes to compensate for the different string characteristics.

If the bridge bevel is symmetrical for its full length (like this ./\. ) then the height method Toad describes is your best bet.

If the bridge bevel is not symmetrical for its full length (like this ./|. ) "usually" the flatter side faces towards the neck.

If the bevel changes along the length of the bridge and the saddle slot is cut perpendicular to the strings and neck, then usually the bridge is set to make the bass E string longer than the treble E string.

To check things after you get it restrung, the harmonic at the twelfth fret for each string should sound the same pitch as when the strings are fretted. If not, then you either have the bridge backwards or need some setup work on the guitar.

~S~