With the global Internet traffic continuously growing, network operators face more and more challenges related to the management of their networks. Efficient utilization of the available network resources becomes crucial to maintain the desired Quality of Service level and control the upsurge in operational expenses. The combination of the Software-Defined Networking concept with the multi-layer network architecture can simplify the process of control and management of the network, its layers, and resources. In this paper, we propose a solution to enhance resource utilization in software-defined multilayer optical networks. The proposed solution takes the advantages of the Software-Defined Networking, Flow-Aware Multi-Topology Adaptive Routing, and Automatic Hidden Bypasses mechanisms to ensure simultaneous, multi-path data transmissions in both IP and optical layers. The Software-Defined Networking controller manages both mentioned mechanisms, selects the best possible bypass, and allocates lightpaths to ensure that the optical spectral efficiency is optimal. The evaluation shows that the proposed solution for multi-layer software-defined network increases the overall network performance and resource utilization.