To date, many studies of air-sea carbon dioxide flux have relied mainly on zonally-homogenous products for the atmospheric concentration of carbon dioxide rather than concurrent measurements of atmospheric carbon dioxide. Several recent studies have investigated the impact of different atmospheric carbon dioxide products on air-sea carbon dioxide flux estimates including differences between zonally-averaged products and more sophisticated products that characterize both meridional and zonal variability of atmospheric carbon dioxide. These studies suggest zonally-averaged products are particularly biased in the coastal seas downwind of industrialized centers such as the East Coast of the continental United States. Inclusion of more ship-based data sets for atmospheric carbon dioxide and methane in the marine boundary layer will improve understanding of sources and sinks both between the atmosphere and ocean and between terrestrial reservoirs and the atmosphere particularly for coastal regions. There are many subtleties involved in developing and implementing atmospheric trace gas systems on ships, particularly concerning drying procedures for sample measurements, pre- and post-deployment linearity checks, water vapor calibrations, and the consistent use of standard gases. Here, we outline a simple yet robust design along with standardized practices for deploying atmospheric trace gas systems on ship platforms, whether on research vessels or commercial shipping routes. We present preliminary results from systems deployed on several ships, including two research vessels operating primarily in high-latitude Northern Hemisphere seas and a commercial ship that traverses the global oceans in both the Northern and Southern Hemispheres.