I left my husband, we have 3 boys , Family Court yes or no?

We agreed on the 2 older boys staying with him and my youngest, soon 6, finishing school, K, and him staying primarily with me then. I don't feel my husband is going to stick with the agreement. So, I went to family court and petitioned for primary custody. Now an attorney told me to do this so my husband can't get me on abandonment. But I heard from other people, that once you go to court, it's a nightmare, especially for the kids. So what do I do now? I don't know anymore. We both want, what's best for our children. Anybody out there any experience with this?