The VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-Rex) was an intensive measurement campaign designed to make observations of poorly understood but critical components of the coupled climate system of the southeast Pacific. This study examines how WRF configuration affects the representation of the marine boundary layer (MBL) and stratocumulus clouds during the campaign, focusing on improvements to persistent low biases in MBL and cloud height. Important configuration choices are related to model spin-up and vertical grid resolution. Chemistry-aerosol simulations are performed using the WRF-Chem CBMZ-MOSAIC model with feedbacks to shortwave radiation and clouds. This simulation uses corrected MOZART boundary conditions, MEGAN biogenics, FIRMS fire emissions using plume rise, and updated anthropogenic emissions, with oceanic DMS emissions and chemistry. Gases and aerosol are evaluated using measurements from VOCALS flights, showing good agreement. Then, cloud properties from WRF-Chem simulations are compared with observations to highlight indirect effects of aerosols on marine stratocumulus. Some of these effects include the increasingly generation of drizzle in the marine remote zone as number of droplets and aerosol decrease; new particle formation from a continental SO2/SO4 plume sitting on the top of the clouds. We propose this WRF configuration for modeling MBLs and stratocumulus clouds on any other marine environments and to evaluate aerosol climate interactions with WRF-Chem on a regional scale.