On most after market units the 'Amp' remote lead is Blue or Blue/White stripe....
Some units have both, (one is remote turn on, one is electric aerial or amplified aerial supply).....
On Sony units the aerial feed generally turns on when the selected source is Radio, and turns off when the selected source is CD or CD changer, (these units will carry a dedicated amp remote)...
The units which carry both will have one running direct into the ISO block, (aerial feed), and one which is simply terminated and left hanging free, (amp remote)....
If you decide to use the aerial feed as a remote turn on source, this can occasionally screw up either radio reception or introduce noise into your system, (classic ground loop issue), in this case either earth all audio to one common grounding point, or switch to alternate remote source......
You fail to state make & model of head unit being used, you also fail to state make, model & year of the car concerned, so I can't really comment on possible cause or possible wiring solution...