What version of Audacity do you have? Please see the pink panel at the top of the page and give us all three Audacity version numbers.
Have you updated to Soundflower 2.0b2? I assume you must have done, or Soundflower would not appear in System Preferences, but see Soundflower 1.66b does not appear in El Capitan [SOLVED] for the link to 2.0b2.
Have you chosen Soundflower 2-ch as Audacity’s Recording Device in Device Toolbar? It should then only record computer playback, unless you have added software that provides playthrough of inputs.
There are mute checkboxes for inputs and outputs in /Applications/Utilities/Audio MIDI Setup.
Gale