Separation anxiety in toddlers

My three year old son has separation anxiety disorder. he is getting better about bedtime but still has the pleading fits that come with the disorder. I want to know the proper way to deal with these fits. some times they last for awhile before he gives up. I usually ignore them then he comes up with excuses and makes me feel bad. Should I continue to ignore him or try to stop the pleading fits and screaming and yelling?