Hi Danny,
Providing you have the loom which runs rear to front for the factory sub, and your Pioneer Headunit has a dedicated sub output, it's very simple.
Take a single RCA lead (you sub out should be mono so you only need to connect to one side - left or right) - cut off the plug from one end to make a short lead and strip the wires so you have the inner insulated wire and the braided screen.
On the plug which comes up from the sub loom you should see the wires as the diagram below;




You need to connect the inner insulated wire on your RCA lead to the White and Black wire on the plug (pin 2), then the screen from the RCA to pin 1, which is a Grey and Black wire, and finally, you need to connect the amp remote wire from your headunit to pin 5 which is the White and Red wire.
Make sure your connections are good - soldered is best - or you may find you get a hum from the sub.

Make sure you set your low pass filter, on the headunit, if you have one for the best results.

One last thought - If you had the 9006 Headunit in the car and the sub wasn't working with that connected, might be worth looking the the sub amp fuse which I think is number 24 in the fuse box under the bonnet.

Good luck, hope you get things sorted.

Pete