You shouldn't have to do anything special when you add more drives.
When you're in EM mode for the install the device is running a stripped down version of the firmware which lives entirely in memory. The change made to that config file should disappear once the device is rebooted.
You can verify what the setting is on your system after the install by running:
java -jar acp_commander.jar -t <device ip address> -c "grep MAX_DISK_NUM /etc/nas_feature"
**you can probably see it in the web interface somewhere too.
Believe it or not I don' t know much about managing disks using the stock firmware. Generally speaking when you add a drive it gets formatted and added to the raid array(s) that contain the boot/system/swap volumes. The options are different when attaching via USB but I'm not familiar with that process. It's probably easier to connect the drive to a different system and copy the data over the network.
If you'd like you can install Debian instead of the stock firmware:
https://github.com/1000001101000/Debian_on_BuffaloYou get a lot more flexibility that way but have to a lot more config for yourself.