Michael Eisner is Chairman of the Board of Directors and the Chief Operating Officer of the company.
Roy E. Disney is Vice Chairman of the Board and President of Disney Feature Animation.
On both counts, as a stockholder and as a corporate executive, Eisner is Roys boss.
Way back before the Dark Times, Roy E. was able to use his personal stock holdings and a huge chunk purchased by the Hunt family to force Walt Disneys son-in-law and his crowd out of the company (long, long history of troubles between the two families). Roy E. hired Frank Wells to run Disney, but they needed someone with Hollywood connections to lend some creditability to Disneys studio operations. They settled on Michael Eisner (who was then a minor executive over at Paramount).
Long story short, the hired help took over the place by stealing the silverware. Eisners own stock holding are huge now and hes managed to put enough allies on the board that hes now immune to pressure to remove him. In the process hes also relegated Roy Disney to a minor figurehead. All either Disney family can do is complain from the sidelines.