Set pickup heights so that the high and low E strings' volumes are relatively the same. This usually means that the high E side of the pickups will be closer to the strings than on the low E side. It may look weird at first, but necessary if you want your string balance to be even. It's probably a good idea to use a compressor when determining the volume balance between the two Es at this point.
You don't usually hear the volume difference from string to string through a regular guitar amp because a guitar amp is not designed to accept full range, flat frequency sources, whereas the Focusrite preamps on their interfaces are known to be quite neutral in terms of sound (a good thing if you want maximum fidelity when plugging in expensive microphones for recording).