If you are looking to run your Python script outside of an ArcGIS for Desktop session using the 64-bit geoprocessing installation, you simply need to run your script in 64-bit Python.
If you are trying to run your Python script without a visible window, simply change the file extension of your script from .py to .pyw. Double-clicking on a pyw file runs the script without a visible shell/command-prompt window.
Replying to this old thread.
Does checking the box Enable for Background Geeporcessing have ArcMap use pythonw.exe instead of python.exe behind the scenes?