The SD card contains either the Nandroid or ClockWorkMod file that contains backups. Otherwise, it does not perform any function for rooting. I'm curious what advantage would be gained by having a two separate SD cards.
Mike
He's asking if he can pop in one SD card and be rooted, pop in another and be non-rooted.
Sundialman, that isn't possible. When you root, you are modifying the actual software on the phone's ROM (read-only memory) chips, not the SD card. The SD card on a Droid doesn't contain the system software at all, just music, pics, videos, application data, etc.
Do you have a reason for wanting to be able to interchange between root and non-root frequently?