The modern, optical bore metro and particularly core networks consist of multiple layers, where multiple different networking technologies are stacked one over the other. In this paper we assume an IP/MPLS layer over an DWDM layer, both controlled jointly by one vertically integrated GMPLS control plane. To better utilize network resources, smaller, upper-layer traffic streams are multiplexed into higher capacity wavelength paths in distributed way throughout the network. This is referred to as grooming. To make the demands better adapt to changing traffic and network conditions we propose the Adaptive Multi-Layer Traffic Engineering (AMLTE) that "tailors" i.e., fragments and defragments wavelength paths in a fully automatic way. Therefore, it adapts very well to changing network and traffic conditions that leads to lower average blocking. Within this AMLTE framework we also implement Dedicated and Shared Protection with two path-pair computation strategies. In this paper we compare these protection scenarios when protection is performed jointly with Traffic Engineering and grooming in a multi-layer network.