A continuous increase in demands from the utility grid and traction applications have steered public attention toward the integration of energy storage (ES) and hybrid ES (HESS) solutions. Modern technologies are no longer limited to batteries, but can include supercapacitors (SC) and flywheel electromechanical ES well. However, insufficient control and algorithms to monitor these devices can result in a wide range of operational issues. A modern day control platform must have a deep understanding of the source. In this dissertation, specialized modular Energy Storage Management Controllers (ESMC) were developed to interface with a variety of ES devices. The EMSC provides the capability to individually monitor and control a wide range of different ES, enabling the extraction of an ES module within a series array to charge or conduct maintenance, while remaining storage can still function to serve a demand. Enhancements and testing of the ESMC are explored in not only interfacing of multiple ES and HESS, but also as a platform to improve management algorithms. There is an imperative need to provide a bridge between the depth of the electrochemical physics of the battery and the power engineering sector, a feat which was accomplished over the course of this work. First, the ESMC was tested on a lead acid battery array to verify its capabilities. Next, physics-based models of lead acid and lithium ion batteries lead to the improvement of both online battery management and established multiple metrics to assess their lifetime, or state of health. Three unique HESS were then tested and evaluated for different applications and purposes. First, a hybrid battery and SC HESS was designed and tested for shipboard power systems. Next, a lithium ion battery and SC HESS was utilized for an electric vehicle application, with the goal to reduce cycling on the battery. Finally, a lead acid battery and flywheel ES HESS was analyzed for how the inclusion of a battery can provide a dramatic improvement in the power quality versus flywheel ES alone.