Rapid mixing stopped-flow experiments, coupled with synchrotron small-angle X-ray scattering (SAXS) on the subsecond timescale, produce a vast amount of experimental structural data. The purpose of this work is to present the key steps of the SAXS data treatment for the case of self-assembly and complexation of cationic lipid particles (vesicles or cubosomes) with plasmid DNA in the course of a rapid mixing stopped-flow process. This approach is significant for the structural analysis of rapidly forming soft-matter biomacro-molecular delivery systems.