In this paper, we investigate the user throughputs of a Cell-Free (CF) system with multiple aerial relay stations (ARSs), where each ARS is defined as an unmanned aerial vehicle (UAV)-mounted relay station. The system operates under a decode-and-forward (DF) protocol and facilitates connectivity between a terrestrial base station (TBS) and terrestrial users. ARSs are equipped with multiple antennas and simultaneously serve users that are outfitted with single antennas and distributed in a specific area. Additionally, a small-cell (SC) system based on the CF structure, where each ARS serves one user with the best channel conditions, is also considered. We analyze system communication in two stages, including user-ARS links and ARS-TBS links, and then we derive expressions for the data rate of users and ARSs. Moreover, we propose the spatial pilot reassignment (SPR) algorithm to optimize pilot assignment, enhancing channel estimation over random pilot assignment methods. The user throughput is evaluated by altering several system parameters, including the with/without data power control, the number of users, the number of ARSs, and the time interval allocated for channel estimation. The results show that the SPR algorithm improves throughput by about 10% compared to the random pilot assignment method at a 90%-likely user throughput, which is equal to a cumulative distribution function value of 0.1.