Self-doped conjugated polymers offer a promising route to simplify processing and enhance stability in mixed ionic-electronic conductors by eliminating the need for external dopants. While they provide advantages in environmental robustness and water-processability, their design remains limited, and key questions about doping efficiency and charge compensation mechanisms are still unresolved. In this study, we report a new class of sulfonated poly(3,4-ethylenedioxythiophene) derivatives with side chains of different lengths (i.e., containing either three or four carbon atoms), designed to systematically explore the impact of molecular structure on self-doping behavior. We find that the material with the shorter, three-carbon side chain exhibits significantly higher electrical conductivity (over 500 S cm-1), enhanced lamellar ordering, and a greater degree of stable polaron formation. Spectroscopic and electrochemical analyses confirm that self-doping is more pronounced in the acid forms and directly influences the fraction of sulfonate groups available for external electrostatic interactions. Upon complexation with a model cationic polyelectrolyte, these materials form homogeneous, amorphous blends that preserve their doping characteristics and electrical performance. This work demonstrates that self-doped sites behave as quasi-permanent ionic-electronic dipoles, maintaining functionality even under ionic crosslinking conditions. Our findings highlight a design paradigm for conjugated polymers that simplifies processing. This approach also enables scalable, water-processable systems for bioelectronics, energy storage, and soft device applications.