Ok CatchMeIfYouCan631 is right, some information I found on this issue on the mustang forums:
* Shaker/Skipper 500 is a 6 speaker setup (4 speakers + 2 front subs);
* each front sub is powered by it's own amp;
* Shaker 500 has only ONE set of sub outputs (i.e. two mono subs running off one set of inputs);
-->This<-- PDF shows the Shaker 500 connection diagram.
Pins 1 & 2 on connector J4 is the mono output of the bass on the Shaker 500, for the Shaker 1000 the rear subs would be 5 & 6 though not show here.
If you look at THIS schematic you can see how the the front sub amps are tied toghter.
So there are two options here.
1. Get a Y-cable that is two male to a single female and tie in the white RCA connector from the Merta harness and tape off the red one.
2. Find the amps and run seperate feeds for the left & right to get stereo bass and only use the Metra harness to turn on the amps.
From what i am reading the amps are behind the drivers side kick panel.