Hello,
I am assuming you are using the NXP EVK and S32 Flasher Tool to flash the device via the UART.
The BMOD pins control the way the device boots from (either from FLASH or SERIAL/CAN) and can only be configured via bootstrap pins (DIP switches on the board) and not possible via any GUI.
The best way for development is for example:
1) To load the application into RAM and execute using a DEBUG probe. (No need to flash and change the BMOD pins every time.)
2) Use the Network Bootloader SW package that allows the customer to update the application via Ethernet every time it's required.
I don't know your requirements, so I am not sure what's best for you to go forward.
Let me know if this helps,
Kind regards,
Pedro Gomes