I think it would be best to always keep the alternator connected to the battery and have a cut-off switch behind these two items. This would prevent the dreaded load-dump which automotive electronics should be rated for, but which is scary none the less. (at least to the EE guys) I'm not sure whether the rules allow this though.
You could catch most of the load dump with a big resistor across the switch like they do in the more expensive switches. I wouldn't know what resistor value they use though.
Igor