So I got a mavic with one battery.  I have another battery on order.  If I update the firmware on the mavic with the supplied battery do I have to do it again in a couple weeks when the second battery comes in.

It depends if there  is a battery update but the app will let you know.
The last firmware update did not have a battery update but the one in the beginning of December did.

If it does need up update the firmware on the battery, it will let you know when you start up the Mavic with the new battery. It won't have to download the firmware again, so the process will be much faster.