I am sure that this has been discussed but I cannot find it ....if there is anyone that knows could you help. I am going to start installing the amp in the rear of the car and will check back today and tomorrow. I have already done the 6x9 so now it is time for the sub.

Let me see if I understand this correctly. You want to install an amp & sub and control the volume of the sub alone using your stock gain control?

Yes that is the plan ...I am sure I have seen someone post that it was possible. Off the 6x9 there is four wire per speaker....when connecting them I only used two so the other two are for the base control. I am guessing that I can use them remaining wires to control sub..

Ok. I can tell you that it can be done for sure.
The best thing to do here is to use a deck that has a fifth channel that is meant for the subwoofer. Then you just run your wire to the gain control, and from there to a mono amp and the sub in the trunk.
However, there is a much simpler way of doing this, without the need for a 5 channel deck. Doing it in this manner, you will inevitably sacrifice some performance. You could hook the sub in parallel with one of your back speakers. In other words - take the two wires that go to one of the back speakers, attach your sub wire to it, run it to the gain control, and then to the amp & sub. Note: this isn't the "proper" way of installing a sub, but I've done it in a '98 Malibu, and it worked just fine for me.
Oh, and don't forget the power cable for the amp, a fuse, and an on/off switch

Why not just get a deck with sub control... sheesh you guys are nuts. :?

All comes down to $$$$$$

I do not want a new deck I like the radio I have and the controls on the steering wheel. I know that there was a way to do it..I mean I am going to try it anyways ...just if someone has done it that would be great. I will test everything thing and make sure not to blow amp up.

Here'* a thought. The factory 6X9'* are dual voice coil and the gain slider controls the woofer section. An aftermarket 6x9 usually has only one pair of inputs. If the amp you intend on using has speaker level inputs then you can use the wires formerly used for the factory woofer as the input of the amp. They are already controled by the gain slider.

Essentially this is the same as what alex_r357 said with the excpetion of the parallel wiring thing.

That is what I thought you should be able to do ...so it should in theory work.
I am going to try it than ....wo ho...lol.

So then would he need to know which color wiring powers the woofer or 2nd voice coil? Or are they just full ranged and a capacitor style cross over is soldered onto the stock speaker leads??