In a preferred implementation, an automated pharmacy admixture system (APAS) prepares intermediary IV bags as drug sources for creating highly diluted patient doses in syringes. During the compounding process the APAS may align needles with a vial seal opening so as to ensure repeated entry through the same vial puncture site via precise control of needle position, needle bevel orientation, and needle entry speed. These techniques can in certain implementations substantially improve bung pressure sealing and reduced particulate generation. The APAS optionally creates drug order queues for incoming drug orders wherein the orders can be sorted by priority, drug type or patient location. A phantom queue can be combined with the incoming drug order queues to include frequently used medicaments to minimize operator loading of the APAS.