Hi, I am having a similar issue. I have found part of the solution:
modify your <project>prj.conf to add your particular Zephyr configuration parameters: In my case I want to add (External) QMSI BSP 1.1.0 to the Zephyr Philosopher example: so I did this:
# These are Zephyr project configuration items - to include the external QMSI BSP...
I am still having issues with the CONFIG_QMSI_INSTALL_PATH parameter, but the above steps are valid.