With counseling and medication, things will get better. It will take time, good things always do, but it is worth the wait.

You don't say if you are newly diagnosed, an old hand, or what you know about the disease. Also, who has custody of the kids? If it's you, then they will know what kind of Mom you really are, and in the long run will be on your side. The current friction between you and the kids may not stem so much from his turning them against you (altho I take your word for it that he is) but from the split in the family and the chaos that causes the children to be acting up.

But yes, in the long run, it gets better. Just hang in there and don't give up until it does.