Designing trajectories to allow for long observation campaigns of planetary moons is not an easy task. Quasi-Satellite Orbits are a type of distant retrograde orbits suitable for Phobos exploration missions, as they offer a convenient means to orbit this moon in the sense of relative motion. MMX (Martian Moons eXploration mission) is a chemical-propulsion sample return mission currently under development at the Japanese exploration agency (JAXA) which plans to make extensive use of QSO (Quasi Satellite Orbits) trajectories during its three-year stay in the vicinity of Phobos. Moreover, the French Space Agency (CNES) contributes to the mission analysis studies of MMX for the Phobos proximity phase in the frame of a larger collaboration between the Japanese and the French agencies, which also includes the delivery of a major payload (MIRS), as well as a rover built in collaboration with the German agency (DLR). Several of the major challenges that MMX teams have to face when building orbital scenarios exhibiting the best trade-off in terms of scientific return, maneuver cost and operational risk will be outlined in this paper. In particular, this work focuses on the contribution of the flight dynamics team at CNES to the design of three dimensional QSO trajectories and their operational use. An overview of the methods implemented to support the choice of suitable spatial trajectories around Phobos, in addition to the design of transfer trajectories, station-keeping and eclipse analyses for 3D-QSO will be presented.