The Atacama Cosmology Telescope observes the Cosmic Microwave Background with arcminute resolution from the Atacama desert in Chile. For the first observing season one array of 32 × 32 Transition Edge Sensor (TES) bolometers was installed in the primary ACT receiver, the Millimeter Bolometer Array Camera (MBAC). In the next season, three independent arrays working at 145, 220 and 280 GHz will be installed in MBAC. The three bolometer arrays are each coupled to a time-domain multiplexer developed at the National Institute of Standard and Technology, Boulder, which comprises three stages of superconducting quantum interference devices (SQUIDs). The arrays and multiplexers are read-out and controlled by the Multi Channel Electronics (MCE) developed at the University of British Columbia, Vancouver. A number of experiments plan to use the MCE as read-out electronics and thus the procedure for tuning the three stage SQUID system is of general interest. Here we describe the automated array tuning procedures and algorithms we have developed. During array tuning, the SQUIDs are biased near their critical currents. SQUID feedback currents and lock points are selected to maximize linearity, dynamic range, and gain of the SQUID response curves. Our automatic array characterization optimizes the tuning of all three stages of SQUIDs by selecting over 1100 parameters per array during the first observing season and over 2100 parameters during the second observing season. We discuss the timing, performance, and reliability of this array tuning procedure as well as planned and recently implemented improvements.