Hi,
You say you have an equalizer - I am not sure where that comes in the signal part from the Phatbox - often the equalizer is connected to outputs from the headunit and then feeds to an amplifier. In that case, adding the isolator between the two will probably not help (but no harm to try). The place that you generally need to put the isolator to elimiate digital "hash" on the audio, and to eliminate alternator whine, etc, is between the Phatbox and the audio component that it connects to (the head unt). This wiki page is specific to a Volvo installation, but using a VW Phatbox, so some of it may help you. Note that the power and audio pins on the 26 way connector are the same, but the control signals will be on different pins in your case.
http://wiki.phathack.com/VW_Phatbox_to_Volvo_Transplant_%28How_To%29Note that you may need to provide alternative power supply grounding arrangements for the Phatbox. I think in VWs it is normally grounded via the head unit cable and the isolator will break the audio ground, and maybe the power ground. You will need to check. Operating the Phatbox with +12V applied and with the control signals connected to the head uniit but with no ground might cause damage, so after installing the isolator I would check the grounding before applying any power and then add a ground wire for the Phatbox if necessary. (That is how I have my Volvo wired.)
Good luck!