Which map application? If it's Maemo Mapper, go to Maps>>Manage Repositories>>Cache DB -- I think that will let you change where they're stored.

As for the partitioning, I'm accustomed to the N800, but for the N810, wouldn't it make more sense to boot from the external card? (By "internal card" I assume you mean the 2GB built-in memory?) You could back everything up -- the system partition using Nokia's backup and the other partition by drag-and-drop with your computer -- and then restore after cloning again.