Flying Capacitor Multi-Level (FCML) converters are attractive solutions for compact power conversion with a large step-down ratio. Many of these applications also need low-voltage auxiliary supplies to power control circuits or subsystems. Rather than build a separate converter that must be rated for the full input voltage, we propose to divert power from a naturally occurring, low-voltage node within the FCML converter itself. The current extracted from this low-voltage node creates a voltage imbalance in the flying capacitors, which, as it is undesirable, degrades the performance of the multilevel converter. Here, we analyze the mechanisms behind this imbalance, and propose a control technique to compensate for the asymmetric operating conditions introduced by the auxiliary power extraction. We demonstrate the control method through simulation and a hardware prototype, achieving excellent flying capacitor balance with a single capacitor voltage measurement and no additional switches or loads.