Basically, you subtract the seam allowance from the patch, enlarge the patch, then add the seam allowance back on.
So, to take a 9" 9 patch block down to 6", each patch starts out as a 3.5" square. Subtract the seam allowance, and you get a 3" square, multiply that by 6/9, and you get 2". Add the seam allowance back on and you cut a 2.5" square.
You have to keep in mind that it's much easier to reduce/enlarge a block to a multiple of the original size.
In the above example, if you wanted to go to a 5" 9 patch, you would have to cut your patches 2.1667 inches. Hmm. so to reduce it to 6" or enlarge it to 18 inches makes more sense, unless you want to paper piece the unit.