This work is dedicated to the design of spacecraft missions to the planets of the solar system and their natural satellites. The problem of construction of quasi-synchronous orbits which pass through a prescribed point over surface of Phobos at prescribed instant of time is considered. The orbits should pass as close as possible to the surface of Phobos at each passage above the planned region of landing. The methods for orbit determination of the spacecraft on trajectory measurements on the background of the working propulsion system are developed. Methods of an estimation of performance errors of dynamic operations at SC flight to a planet-purpose for cases of use of chemical and low-thrust engines are developed. Those methods take into account prediction errors of spacecraft motion, the performance errors of impulses, non-gravitational perturbations, etc. The methods are based on the experience of ballistic and navigational support missions to Venus: Venera 15/16 missions, Vega missions; to Mars: the spacecraft Phobos-2. The methods were applied for the project Phobos-Grunt, as well as the design of flight to the Moon for the projects Luna-Resurs and Luna-Glob; to the Venus for the projects Venera-D, to system of Jupiter for spacecraft landing on the surface of its natural satellite Europe.