Resonant soft X-ray scattering was used to determine the presence of more subtle orderings not detected in standard structural analyses. By tuning to specific Co absorption edges, arrangements particular to the electronic states of those elements are enhanced. We have discovered an ordering commensurate to the lattice at the ($frac{1}{4}~frac{1}{4}~frac{1}{4}$) position. Incommensurate peaks near this position were also observed. The intensity of these peaks depends on the oxygen concentration of the sample, and can be suppressed at temperatures above 320 K. Regular orderings of charge density which closely match the underlying lattice may help to explain the observed propensity for SrCoO$_{3-y}$ (0 $leq$ y $leqfrac{1}{2}$) to stabilize at particular phases.