Most Perko can be switched between 1, both, 2 while running; just don't over shoot/turn the wrong direcction to Off.
If you have a 3 wire alt there is a more expensive model with a field disconnect that can minimize the chance of damage but it is best to not go there regardless.

The way Perko sets up their order: off, 1, all, 2; overshooting is very unlikely as 1 is usually the start battery so as long as you turn the correct direction to charge while leaving, you will be fine.

Check you model number before making this ASSUMPTION.