In our previous work [J. Chem. Theory Comput. 2013, 9, 4959], we introduced the PYXAID program, developed for the purpose of performing nonadiabatic molecular dynamics simulations in large-scale condensed matter systems. The methodological aspects and the basic capabilities of the program have been extensively discussed. In the present work, we perform a thorough investigation of advanced capabilities of the program, namely, the advanced integration techniques for the time-dependent Schrodinger equation (TD-SE), the decoherence corrections via decoherence-induced surface hopping, the use of multiexciton basis configurations, and the direct simulation of photoexcitation via explicit light-matter interaction. We demonstrate the importance of the mentioned features by studying the electronic dynamics in a variety of systems. In particular, we demonstrate that the advanced integration techniques for solving TD-SE may lead to a significant speedup of the calculations and provide more stable solutions. We show that decoherence is necessary for accurate description of slow relaxation processes such as electron-hole recombination in solid C60. By using multiexciton configurations and direct, nonperturbative treatment of field-matter interactions, we found nontrivial optimality conditions for the multiple exciton generation in a small silicon cluster.