We describe our work on trapping, cooling and detecting mixed ion species for a scalable ion trap quantum information processing architecture. These mixed species chains in linear RF traps may help solve several problems with scaling ion trap quantum computation to large numbers of qubits. Initial temperature measurements of linear Coulomb crystals containing barium and ytterbium ions indicate that the mass difference does not significantly impede sympathetic cooling of normal modes that couple well to the coolant ions (Ba in our case). Average motional occupation numbers are estimated to be 10 to 20 quanta per mode for these well cooled modes for chains with small numbers of ions, consistent with the Doppler limit temperature. For normal modes that do not couple significantly to the coolant atoms, the occupation numbers are significantly higher, of order several thousand. Strategies for better cooling of these modes are discussed. Further, we are working to implement these techniques in microfabricated surface traps in order to exercise greater control over ion chain ordering and positioning.