Current flow is one way, and electron flow is another. In school, they showed current coming out of the positive pole and returning to the negative pole. Alternating current is the same way, however, the poles reverse multiple times per second, so the current flow reverses as the poles change.
You should fuse the side that is not grounded or common. Direction of current flow has nothing to do with it. If you touch a voltage terminal, you don't care if the current is flowing from feet to fingertip or finger tip to feet, either way will kill you. You fuse the ungrounded parts because it is assumed you are standing on the grounded parts and you want the ungrounded parts de-energized after a fuse blows or breaker is tripped.