On a standard floyd (and this is only some manufacturers... not all, so there's not any real "standard..."), which has 3 pairs of different height saddles, the orientation should be:
1 2 3 3 2 1
e b g D A E
This allows for the proper radius to follow the curvature of the neck. You can always shim them if you need to get more height or a different arc, but if they're on the guitar they came with it's usually not necessary.
Also note -- a standard floyd has a radius coming in somewhere in the neighborhood of 10" to 12" -- nowhere near as flat as any
Edge bridge. So you might wanna check to be sure somebody didn't slap the wrong saddles into your bridge.
ryan