Hey,
Make sure you are using the right place to hook up the sub. If it's a processor loop or tape loop it is not the right place.
Next, your sub should have a high and low pass filter, so if you take the output from it to your amp you should reap the benefits.
If your main speakers are proted, seal them by plugging the holes in the back with unneeded t-shirts or socks. You don't ahve to fill them, just plug them tight.
Otherwise, if it was me I'd use a miniDSP to do this all, along with the right measurement software. :)