Kinodynamic RRT planners are considered to be general tools for effectively finding feasible trajectories for high-dimensional dynamical systems. However, they struggle when holonomic constraints are present in the system, such as those arising in parallel manipulators, in robots that cooperate to fulfill a given task, or in situations involving contacts with the environment. In such cases, the state space becomes an implicitly-defined manifold, which makes the diffusion heuristic inefficient and leads to inaccurate dynamical simulations. To address these issues, this paper presents an extension of the kinodynamic RRT planner that constructs an atlas of the state-space manifold incrementally, and uses this atlas both to generate random states and to dynamically steer the system towards such states. To the best of our knowledge, this is the first randomized kinodynamic planner that explicitly takes holonomic constraints into account. We validate the approach in significantly-complex systems.