When I put my player in the car I cannot seem to restore my visuals configuration.

It's in the FAQ. Short answer, you have to install Hijack to do this. (Unless I misunderstand your problem.)

Why do the tracks play in different order to how I have set the playlist order using emplode?

Are you sure you've changed the true ordering of the playlist, or have you just sorted the tracks in emplode to display in that order (which can be a different order than they're played on the player)?