Dissociation is a significant complication for EMDR, and a lot of therapists may think that EMDR can't be done with a patient who dissociates. There is a new book, by Sandra Paulsen, on using a combination of Ego State Therapy and EMDR, also drawing from other modalities, specifically for treating trauma and dissociation. The book is for EMDR therapists and for clients too. I haven't read much of it yet, but it could be helpful for you and to share with your therapist. It looks like a good one.

The book is: Looking Through the Eyes of Trauma and Dissociation: An illustrated guide for EMDR therapists and clients.