When not yet creating a custom board, I simply copy the config file and put it somewhere inside the workspace. If you eventually create a custom board, you can then place it in the proper directory (board/configs/*/defconfig). Doing it this way also allows you to configure nuttx with my framework using the "make configure" command.
configure.sh works with board directories that are outside of the source tree as well. You never have to put a custom board configuration in the repository's boards/ sub-directory. Instead of
tools/configure.sh <board>:<config> Use tools/configures.sh <path to the custom board defconfig directory>
