This paper presents techniques to store, manipulate, and detect cluster ions in an rf Paul trap as an approach to study the physics and chemical physics of clusters. The trap has been designed to be the primary experimental environment in the sense that experimental manipulation and ion detection are performed in situ within the trap. Specific design considerations for the trap and rf electronics relevant to metal cluster experiments are discussed. We present the application of these techniques to measurements of trapped C-60(+) in order to estimate their limitations for studying metal cluster ions. This paper demonstrates the capability to nondestructively detect small variations in the number of trapped C-60(+) ions with an ion noise level of approximate to 100 ions limited by thermal current fluctuations. Trapped ion lifetimes of tau(ion)>30 min are measured following the relaxation of C-60(+) translational energy to approximate to 300 K. Measurements of the collisional dissociation of trapped C-60(+) ions at rates <100 s(-1) by He at similar to 10(-6) Torr have been performed and the products detected in situ by the mass distribution of the C-n(+) products. Several possibilities for metal cluster experiments in rf Paul traps are discussed.