Modern Deep Neural Networks (DNNs) exhibit profound efficiency and accuracy properties. This has introduced application workloads that comprise of multiple DNN applications, raising new challenges regarding workload distribution. Equipped with a diverse set of accelerators, newer embedded system present architectural heterogeneity, which current run-time controllers are unable to fully utilize. To enable high throughput in multi-DNN workloads, such a controller is ought to explore hundreds of thousands of possible solutions to exploit the underlying heterogeneity. In this paper, we propose OmniBoost, a lightweight and extensible multi-DNN manager for heterogeneous embedded devices. We leverage stochastic space exploration and we combine it with a highly accurate performance estimator to observe a x4.6 average throughput boost compared to other state-of-the-art methods. The evaluation was performed on the HiKey970 development board.