The phase separation of aqueous polymer solutions is a widely used method for producing self-assembled, membraneless droplet protocells. Non-ionic synthetic polymers forming an aqueous two-phase system (ATPS) have been shown to reliably form protocells that, when equipped with biological materials, are useful for applications such as analyte detection. Previous characterization of an ATPS-templated protocell did not investigate the effects of its biological components on phase stability. Here we report the phase diagram of a PEG 35k-Ficoll 400k-water ATPS at baseline and in the presence of necessary protocell components. Because the stability of an ATPS can be sensitive to small changes in composition, which in turn impacts solute partitioning, we present partitioning data of a variety of nucleic acids in response to protocell additives. The results show that the additives-particularly a mixture of salts and small organic molecules-have profound positive effects on ATPS stability and nucleic acid partitioning, both of which significantly contribute to protocell function. Our data uncovers several new areas of optimization for future protocell engineering.