\documentclass[monochrome]{fithesis3}
\usepackage{ifluatex}
\ifluatex
  \usepackage{polyglossia}
  \setmainlanguage{czech}
\else
  \usepackage[czech]{babel}
\fi
\thesissetup{
  faculty=fss,
  gender=m}
\begin{document}
  foo bar
\end{document}
