The N.C. Ecosystem Enhancement Program today announced that Michael S. Ellison of Cary will assume the duties of EEP deputy director on Nov. 29.   Ellison, 48, comes to EEP from BHE Environmental Inc., where he served as vice president and director of natural resources.   Ellison is a 1990 graduate of the University of Alabama.  As deputy director, Ellison will be responsible for day-to-day duties of operations management.