Well, IE refers to the current and extinct languages that are descended from PIE. PIE has been also divided into earlier and later phase. When you look at the appendix in the A-H dictionary, the roots given are reconstructed PIE roots.
Well, I suppose that PIE itself is an extrapolation from the recorded IE languages backwards in time to about 6000 BCE. Some folks (today usually called Nostraticists) try to extrapolate further back in time from PIE and Proto-Semitic (the reconstructed parent of Hebrew, Arabic, Ethiopian, et al) and other proto-languages to Nostratic. Others say that 10,000 years BP is about as far back as the historical-comparative method can take you. The enmity between these two groups is rather intense. [Full disclosure, I fall into the anti-Nostraticist group, but try not to get drawn into flamewars with the pro-Nostraticist group.]
