You will be surprised how much difference it makes if you have the subwoofer in the right location. For all you could know at a certain frequency you may have a null. Right lets start again if you don't mind. Do you have some photos off your room where the sub is located.
Also I would take some time to read up on this side of the forum to get some ground info on the Room EQ Wizard program to get some basic information on how it works and the benefits are had from using it. http://www.hometheatershack.com/forums/rew-forum/
In this forum you can go through the guides on what equipment you need etc..
I can help you with this with what ever questions you have but it is good for you to read up on it because believe me the benefits are massive.
Understanding how you EQ your sub is a big major factor in your system.