Large Eddy Simulations (LES) and experimental measurements are performed to examine different aspects of a supersonic multi-stream jet representing a canonical airframe-integrated variable cycle engine architecture. The flowfield consists of two streams separated by a splitter plate; an upper supersonic core stream (Mach = 1.6) and a lower bypass stream (Mach = 1), which exit onto an aft-deck plate. Previous experimental and numerical efforts have shown that an instability associated with the splitter plate trailing edge exhibits a global influence on the flow because of its interaction with the shock train. The instability is also responsible for impairing the effectiveness of the bypass stream as a thermal and acoustic barrier between the core jet and the airframe. In the first part of this study, the potential for passive flow control by introducing sinusoidal spanwise modifications along the splitter plate edge is explored. The underlying mechanisms are explored computationally using LES on a simplified configuration that isolates the splitter plate. Results on two different spanwise wave numbers indicate that the sinusoidal trailing edge induces streamwise vorticity, which enhances mixing between the two streams and breaks up the shed structures seen previously. The tone is suppressed, together with small changes in the mean shock locations and shear layer trajectories. These spanwise modifications are in the process of being tested in the experimental facility using the full multi-stream nozzle. In a complementary effort, geometric modifications to the aft-deck and its effects on the flowfield are examined experimentally using the actual test rig. Results on the nominal deck length are compared with those from a half and double length deck, and without the deck. In each case, the shock train initiated at the SERN persists, and influences the downstream plume development. Although the impact on the tone is relatively small, the plume itself shows perceptible change. The extended deck results in a small downward movement of the plume relative to the nominal length, while the half nominal length displays larger spread of the lower shear layer initiated at the deck edge. Current efforts are focused on using the results to target complementary simulations and experiments for each tested modification.