This paper investigates the model-based nonlinear control of a class of soft continuum pneumatic manipulators that bend due to pressurization of their internal chambers and that operate in the presence of disturbances. A port-Hamiltonian formulation is employed to describe the closed loop system dynamics, which includes the pressure dynamics of the pneumatic actuation, and new nonlinear control laws are constructed with an energy-based approach. In particular, a multi-step design procedure is outlined for soft continuum manipulators operating on a plane and in 3D space. The resulting nonlinear control laws are combined with adaptive observers to compensate the effect of unknown disturbances and model uncertainties. Stability conditions are investigated with a Lyapunov approach, and the effect of the tuning parameters is discussed. For comparison purposes, a different control law constructed with a backstepping procedure is also presented. The effectiveness of the control strategy is demonstrated with simulations and with experiments on a prototype. To this end, a needle valve operated by a servo motor is employed instead of more sophisticated digital pressure regulators. The proposed controllers effectively regulate the tip rotation of the prototype, while preventing vibrations and compensating the effects of disturbances, and demonstrate improved performance compared to the backstepping alternative and to a PID algorithm.