We present new, high angular resolution (~0.22) MERLIN observations of neutral hydrogen (HI) absorption and 21-cm radio continuum emission across the central ~900 parsecs of the ultraluminous infrared galaxy, Arp220. Spatially resolved HI absorption is detected against the morphologically complex and extended 21-cm radio continuum emission, consistent with two counterrotating disks of neutral hydrogen, with a small bridge of gas connecting the two. We propose a merger model in which the two nuclei represent the galaxy cores which have survived the initial encounter and are now in the final stages of merging, similar to conclusions drawn from previous CO studies (Sakamoto, Scoville & Yun 1999). However, we suggest that instead of being coplanar with the main CO disk (in which the eastern nucleus is embedded), the western nucleus lies above it and, as suggested by bridge of HI connecting the two nuclei, will soon complete its final merger with the main disk. We suggest that the collection of radio supernovae (RSN) detected in VLBA studies in the more compact western nucleus represent the second burst of star formation associated with this final merger stage and that free-free absorption due to ionised gas in the bulge-like component can account for the observed RSN distribution. (Abridged)