A set of Observing System Simulation Experiments (OSSEs) are performed to assess the impact of assimilating Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) electron density profiles and ground-based Global Navigation Satellite System (GNSS) total electron content (TEC) observations in a whole atmosphere data assimilation system. The OSSEs are performed using the Whole Atmosphere Community Climate Model with thermosphere-ionosphere eXtension (WACCMX) with data assimilation provided by the Data Assimilation Research Testbed (DART) ensemble adjustment Kalman filter. Results from the OSSEs demonstrate that the assimilation of ionosphere observations improves the short-term (1 hr) forecasts and analyses. The OSSEs show that the short-term forecasts and analyses are further improved when the ionosphere observations adjust the thermosphere neutral composition and temperature in addition to the ionosphere electron density. Based on an initialized forecast experiment, we find that adjusting the thermosphere neutral composition and temperature also leads to improved forecast skill in the ionosphere on longer time scales (i.e., beyond 1 hr). Additionally, it is shown that using a 1 hr data assimilation cycle, and removal of second-order divergence damping in WACCMX+DART significantly improves tidal amplitudes, which were previously found to be too small. These initial results represent the first whole atmosphere data assimilation system with capabilities to assimilate observations from the troposphere to the ionosphere-thermosphere.