A digital frequency multiplexing (DfMUX) system has been developed and used to tune large arrays of transition edge sensor (TES) bolometers read out with SQUID arrays for mm-wavelength cosmology telescopes. The DfMUX system multiplexes the input bias voltages and output currents for several bolometers on a single set of cryogenic wires. Multiplexing reduces the heat load on the camera's sub-Kelvin cryogenic detector stage. In this paper we describe the algorithms and software used to set up and optimize the operation of the bolometric camera. The algorithms are implemented on soft processors embedded within FPGA devices operating on each backend readout board. The result is a fully parallelized implementation for which the setup time is independent of the array size.