To use in text citation for the poem, follow MLA guidelines.
Here is a great link to an online writer’s handbook with a searchable index to figure out what format to use when citing different print and online media.
For the purposes of this paper, you can quote the poem like standard literature, rather than set-off lines of poetry, unless you are citing a large passage.
Below is an example from a really great article, written by Arthur A. Brown, of how to incorporate quotations from the poem into your essay:
The Epic of Gilgamesh opens with the convention of a frame — a prologue that sets off the story of Gilgamesh’s life. An unnamed narrator states, “I will proclaim to the world the deeds of Gilgamesh” (61). Thus the narrator introduces himself before he introduces the hero, and by doing so, welcomes us, as the imaginary listeners and actual readers, into the endless present of the telling of the tale. The deeds of Gilgamesh took place in the past. Having returned from his journey and resting from his labor, Gilgamesh, the narrator recounts, engraved the whole story on a clay tablet. What we are reading, then, is the transcription of an oral telling that repeats a written telling. On the one hand the frame helps verisimilitude. By referring to Gilgamesh’s own act of writing, the narrator attempts to convince us that Gilgamesh was an actual king and that the story that follows is a true story. On the other hand, by calling our attention to the act of telling, the narrator reminds us that the truth of a story might lie in the very fact of its being a story — the undeniable fact of its narration. To deny its narration would be to deny our own existence. Either way, the frame blurs the distinction between Gilgamesh’s world, or the world of the tale, and our own.
Sandars, N. K., trans. The Epic of Gilgamesh. London: Penguin, 1972.
*****FYI: You can read the rest of this essay here.