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In this paper, we present an automation technique that yields high-performance, low-cost optoelectronic alignment and packaging through the use of intelligent control theory and system-level modeling. The control loop design is based on model-based control, previously popularized in process and other control industries. The approach is to build an a priori knowledge model, specific to the assembled package's optical power propagation characteristics, and use this to set the initial "feed-forward" conditions of the automation system. In addition to this feed-forward model, the controller is designed with feedback components, along with the inclusion of a built in optical power sensor. The optical modeling is performed with the rigorous scalar Rayleigh-Sommerfeld formulation, efficiently solved online using an angular spectrum technique. One of the benefits of using a knowledge-based control technique is that the efficiency of the automation process can be increased, as the number of alignment steps can be greatly reduced. An additional benefit of this technique is that it can reduce the possibility that attachment between optical components will occur at local power maximums, instead of the global maximum of the power distribution. Therefore, the technique improves system performance, while reducing the overall cost of the automation process.