There is a need to drastically reduce greenhouse gas emissions. While significant progress has been made in electrifying transport, heavy duty transportation and aviation are not likely to be capable of electrification in the near term, spurring significant research into biofuels. When coupled with carbon capture and storage, biofuels can achieve net-negative greenhouse gas emissions via many different conversion technologies such as fermentation, pyrolysis, or gasification to produce ethanol, gasoline, diesel, or jet fuel. However, each pathway has a different efficiency, capital and operating costs, and potential for carbon capture, making the optimal pathway dependent on policy and spatial factors. We use the Integrated Markal-EFOM System model applied to the USA, adding a rich suite of biofuel and carbon capture technologies, region-specific CO2 transportation and injection costs, and government incentives from the Inflation Reduction Act. We find that under current government incentives, biofuels and carbon capture from biorefineries are primarily focused in the Midwest and South of the USA, but play a relatively small role in the overall USA transportation sector even in 2055. However, increased government incentives, biomass availability, or oil price could lead to increased biofuel production and reduced transportation emissions.