If she is untreated and unwilling to admit that she has a problem that needs to be dealt with through medication and therapy, there is nothing that you can do to ever make the situation better.
This is just my opinion but I have some experience. The leaving and coming back seems to be very common. The mania sets in, they think that you are the enemy and are holding them back. They run away to live the life they dream of. Then when they come back down they realize how important and special you were and want you back. Untreated, this cycle will just continue to happen.
I'm at the end of my marriage to my wife with BP. I know I wanted to do everything I could to keep the marriage together and stay with her, both out of a sense of duty, and for my daughter. I imagine you might be feeling this too. Its difficult to admit defeat because it feels like you have failed, even though you haven't. Marriage to a person with BP is like playing a game where you think you know the rules, you think you are winning, only to find out the rules changed six months ago and no one bothered to tell you.
All I can say is that it is incredibly hard being the spouse of a person with BP, and you should not feel guilty in letting her go and moving on for the sake of your children and yourself. As much as it might hurt now, there will be a future without her where you and your children can experience the things you deserve.