Popov, Rögl, Rozanov, Steininger, Schcerba and Kovac Eds. 2004, Lithological-Paleogeographic maps of Paratethys. 10 maps Late Eocene to Pliocene, Courier Forsch. Inst. Senckenberg. They deal with
Fortunately I'm already in contact with Sergei Popov and he is helping me with this issue. Thank you very much for your information because it is actually what I was looking for.
Actually, what you need is a plate model first. Fossil data should be plotted (in GIS) on present day maps. Then you reconstruct them back to a specific time period (Cenozoic is too broad). The second overlay is the depositional environments followed by the paleotopography/bathymetry. You can, in this way, also test the validity of the paleoenviromental maps.