The Joint Operational Energy Initiative (JOEI) models energy (and all classes of supply) consumption, generation, and sustainment across a virtual battlefield area of operations utilizing the System of Systems Analysis Toolset (SoSAT) and the Fully Burdened Cost Tool (FBCT). Recent advances in SoSAT provide a capability to model condition-based scenarios that better represent complex dynamic scenario changes and provide more accurate, realistic operational scenario and sustainment modeling. In addition, the JOEI team developed a new operational metric called Combat Effective Operational Endurance (CEOE) using SoSAT system-level outputs to determine unit combat power over time based on system availability and system combat weights. FBCT improvements include increased synchronization with SoSAT and expansion of capabilities to model Class V (ammunition), Class VII (major end item) transport, troop movement, convoy generation and higher fidelity cost allocation. The new SoSAT condition-based scenario capability and FBCT Class-VII capability were recently used by the JOEI team to model dynamic transport operations for crew and equipment transportation and resupply convoys in Phase II operations. Example results for a trailer study involving the Phase II model and for the new CEOE metric are presented.