Sounds like you have done things right so far by leaving extra wood around the knot. In the absence of pics, a little more info would be needed:
Looking at the bow lengthwise, where does the knot fall? Is it in the handle area, for example, or in the middle of one of the limbs? Looking at the bow widthwise, where is the knot? Is it at an edge of the bow, or in the middle. A description of the overall bow is also needed---its length, width at fades, profile (straight or reflexed, for example), and what you are hoping to get in terms of draw length and weight.