A methodology for designing single-flux-quantum (SFQ) flip-flops composed of both conventional (0-) and π-shifted Josephson junctions is investigated. We investigated the implementation of a storage loop, which can store flux quantum and is indispensable to express binary logic states in superconductor logic circuits. As all SFQ flip-flops have storage loops, the investigated design methodology can be applied to their design. We designed several SFQ flip-flops composed of 0- and π-shifted Josephson junctions using the investigated design methodology. The performances of the designed SFQ flip-flops were quantitatively evaluated by using an analog circuit simulator which we developed. We confirmed the correct operation of various SFQ flip-flops composed of 0- and π-shifted Josephson junctions with wide operating margins. Moreover, we observed that the investigated design methodology is suitable for SFQ flip-flops with complementary outputs because a storage loop composed of both 0- and π-shifted Josephson junctions has a symmetric structure and the complementary output function can be realized by using the storage loop. Our investigation indicates that the number of Josephson junctions and static power consumption of a non-destructive read-out flip-flop with complementary outputs (NDROC) can be reduced to less than half of those of the conventional NDROC, which has two storage loops composed of 0-Josephson junctions, to realize the complementary output function. The investigated design methodology is expected to be applied to not only SFQ circuits but also other superconducting logic circuits and novel reconfigurable logic devices using programmable 0-π Josephson junctions.