It will add, not change. The cross compiled libs get their own versioned directory e.g. /usr/lib/fpc/3.3.1/units/x86_64-win64/ , /usr/bin/fpc/3.3.1/x86_64-win64/ etc.(there may be minor differences, depending on platform)
You can write some simple shell scripts to switch between versions.
Note that the bin directory may be simply /usr/bin but that can be configured to the above. for cross compiling with a single version that does not matter too much since the core compiler is always called ppcross<platform>, unless you rename it yourself.