The Forerunner(s), being an incredibly advanced species, did not fear the Flood enough to destroy them, and instead kept them contained within Halo for study. They, of course left Halo, to ensue greater archeological discoveries elsewhere. The Covenant found Halo and studied it, finding deep religious significance in it. As Cortana said, "The control room seems to be located in some sort of temple, or shrine." The Covenant revered the long since gone Forerunner(s) because of the incredible advancement of Halo. They dug deeper inside to see if they could find more religious leavings of the Forerunner(s). They instead found the Flood. The symbols on the walls of the building in 343 Guilty Spark are the same as the ones on the Covenant's vehicles, as well as on the Elites backs. (This I have only heard of and have not yet found to be true myself) I assume that this is not because the Covenant are the descendants of the Forerunner(s), but because they revere them. A Forerunner symbol on an Elite's back would be the same as the American flag on the marines shoulders, by my estimation. The only reason the some of the Covenant technologies are similar to the Forerunner(s), such as the Library elevators and the Shade guns, are because the Covenant emulated the Forerunner(s).