1. Without implementation of the Keating potential into ATK, you cannot impose the calculator to do simulation with such potential. This is quite obvious.
Choose one of the available classic potentials especially for Si, Ge, and H.
2. For thermal conductance calculations, you need to think about which contributions you want to calculate. The NEGF and NEMD in ATK are suitable and efficient for the calculation of the phonon thermal conductance by using the classic potentials. In my personal point of view, the SE method may be suitable for the electronic properties (e.g, the electronic transport) of large system, and unsuitable for the phonon of lattice because the parameters in the SE model are mostly optimized from the electronic structures of some bulk materials. If you want to simulate the thermal conductance of electrons in a device by using NEGF, the use of NEGF+SE may be a good choice.
3. There are some open source tools (e.g., BoltzTraP and ShengBTE) for the phonon or electron thermal conductance by post-processing the DFT output (such as forces or eigenvalues) and based on the Boltzmann Transport equations. You can write your own interface between ATK and these tools for the calculations of thermal conductance.