The "Base Code" for the new Facebook Pixel can be placed in the Settings section > Edit for Policies, Addenda, Disclaimers section > Tracking Code box. Or into the Layout section > Edit for Advanced Layout > Head Addendum box. Code entered into either of these fields will be placed on every page in the store.
The "Standard Event Code" should be placed in the Settings section > Policies, Addenda, Disclaimers section > Order Affiliate Addendum box (same place any existing FB conversion code should be). Code entered here will fire when an order is submitted.
Note: The Order Affiliate Addendum Question mark contains a list of variables that can be used to send specific order information to facebook.