You should be storing these files into separate folders. You can do this by going in wyBuild, clicking File -> Properties -> and the "wyUpdate" tab. Then change the output folder for wyUpdate. For example change it to "Product 1\wyUpdate". Do the same for the updates output by going into the "Update & server files" tab and changing the output folder to "Product 1\Updates".
Do this for each of your products.
Does this make sense?