Thank you very much for replying. The current documentation implies that control allocation is done using mixer files exclusively. However I now understand that geometry files are an important step in the process and they are used together with the mixer files like @bkueng explained. Following the steps as explained in the following slide (recommended by @jlecoeur) :
I was able to create a quadrotor mixer file correctly and have stable flight.
Thanks @bkueng @jlecoeur