E.E.P was an abbreviation visible on the blast door map. The expansion of the acronym to Emergency Escape Protocol was confirmed in the official Lost jigsaw puzzles.
Clear references on the blast door map:
These references suggest that the E.E.P. was a series of subterranean conduits possibly leading to the Arrow. Indeed, the map showed many interconnected tunnels, as did the DHARMA cabling map found by Sayid at the Flame.