You need to read Colorado Bulldog's thread. His wife is pulling pretty much the same stunts and somethings that are even worse. You are right though. If you keep doing what you're doing with your boys, they will know without a doubt that there is only 1 Dad. It really doesn't matter what your W tells them. They WILL know!
Make sure you always have your name on their records concerning school and any outside activity they may be involved in. Judging from what you've written, you don't want to hear how your kids are doing through the grapevine. You do have rights but you might have to fight her for them and remind her from time to time.
Hopefully when this relationship with OM runs it's course, (as eventually it will) communication will get easier. In the meantime keep doing what you're doing. You are a great Dad!