Generally, problems regarding self-esteem and self-efficacy are caused by earlier events which gave negative lessions regarding worth, power, lovability, etc. These earlier perceptions appear to be stored in the brain with the same affects, beliefs, physical sensations, etc. as existed at the time they were originally experienced. These are the "touchstone" memories which are responsible for present reactions and feelings of self-denigration. As these memories are processed, the client learns what is useful, and is able to discard the rest. The increased feelings of self-worth and self-efficacy are natural concomitants of successful processing.
The clinician*s job is to identify the specific maladaptive behaviors, beliefs, reactions, etc. Then for each presenting complaint, the appropriate targets are processed. Specifically, EMDR is used to process the earlier memories that laid the groundwork for the problem, and the present conditions that trigger the dusturbance, and to help incorporate the needed skills and behaviors for the future. A good resource for a general overview is the book EMDR (Shapiro & Forrest, 1997, BasicBooks) which gives specific cases and transcripts.