Although I have been searching for this answer online for quite some time, I could not find a single answer to this question.
When i run cmake on a CMakeLists.txt file I have, all the generated files are created next to the project file.
If i add a -B arg, the generated files are created within the specified directory.
What is the best way to define that -Bbehavior inside the CMakeLists.txt?
You don't define it inside CMakeLists.txt and in fact you cannot because it is already determined before CMake code starts running.
The usual way to save preferred configure command line options is via presets: https://cmake.org/cmake/help/latest/manual/cmake-presets.7.html
I use that
add_custom_command(TARGET ${PROJECT_NAME} POST_BUILD
COMMAND ${CMAKE_COMMAND} -E copy_directory
${CMAKE_SOURCE_DIR}/res $<TARGET_FILE_DIR:${PROJECT_NAME}>/res)