Hi Brian,
first, could you please upgrade to SEC v9? It brings multiple improvements, including custom hooks which should allow you to be able to add custom scripts without modifying the main build/write scripts created by SEC tool.
SEC tool allows "additional" images to be flashed together with the main application, which might be handy for your use case.
Using custom "hooks" scripts you can execute your scripts during build & write at different phases of the scripts, without modifying the generated scripts, so special cases not supported by SEC tool can be implemented more easily while still using generated scripts from SEC tool.
Could you please describe your use case, what exactly you want to do in SEC tool?
Regards,
Libor