There is a documentation file included in the simulator, /documentation/LTEsystemDoc.pdf, that mostly explains the features of the simulator. A video tutorial on the use of the simulator can be found here, https://owncloud.nt.tuwien.ac.at/index.php/s/8rLEQsU1w2UkJtl
Regrading the 3D model, these two papers explain the step-wise implementation
F. Ademaj, M. Taranetz and M. Rupp, “Implementation, validation and application of the 3GPP 3D MIMO channel model in open source simulation tools,” 2015 International Symposium on Wireless Communication Systems (ISWCS), Brussels, 2015, pp. 721-725. doi: 10.1109/ISWCS.2015.7454444
F. Ademaj, M. Taranetz, M. Rupp:
“3GPP 3D MIMO Channel Model: A Holistic Implementation Guideline for Open Source Simulation Tools”; EURASIP Journal on Wireless Communications and Networking (invited), 2016 (2016), 55; 14 pages.