This paper presents a method for solving the dynamic equations of multibody systems containing both rigid and flexible bodies. The proposed method uses independent coordinates and projects the dynamic equations on the constraint tangent manifold by means of a velocity transformation matrix. It can be used with a wide variety of integration formulae, considering both fixed and variable stepsizes. Topological semirecursive methods are used to take advantage of the relatively small number of parameters needed. An in depth implementation analysis is performed in order to evaluate the terms involved in the integration process. Numerical and stability issues are also discussed.