Recently, network operators started implementing traffic engineering (TE) techniques in their network. These TE techniques typically involve a single layer (for example, the IP/multi-protocol label switching (MPLS) layer). Although single-layer TE (STE) can improve the network performance (e.g., throughput, quality of service (QoS)), this improvement is bounded by the available capacity in that network layer. The evolution towards intelligent optical networks (IONs) allows further increasing the improvements achievable by the TE techniques, by involving more than one layer in the TE actions. Multi-layer TE (MTE) occupies network resources in a smart way and optimizes the QoS since it dynamically reconfigures the logical topology in the upper layer by properly updating the optical connections in the underlying optical layer. However, the performance of the network is impacted by the configuration scheme adopted by MTE. Therefore, in this paper, we focus on analyzing the influence of the MTE configuration scheme on the MTE behavior, and evaluate the network performance by studying simulation results obtained from a realistic IP-over-ION network.