Here is a simple way of doing it. The following code is a minimalist .sty file called yourpackagename. It defines a switch \ifyourpkgprefix@enoption and declares an option called en which, if passed to your package, sets the switch to true. After the option(s) have been processed, the babel package is loaded with options english and czech in the desired order, on the basis of the switch's value.
Of course, you should choose different package name, prefix, description, etc.
\NeedsTeXFormat{LaTeX2e}
\ProvidesPackage{yourpackagename}[2014/01/05 v0.1 yourpackagedescription]
% switch for 'en' option
\newif\ifyourpkgprefix@enoption\yourpkgprefix@enoptionfalse
\DeclareOption{en}{\yourpkgprefix@enoptiontrue}
\DeclareOption*{\OptionNotUsed} % discard any undeclared option
\ProcessOptions\relax
\ifyourpkgprefix@enoption
\RequirePackage[czech, english]{babel}
\else
\RequirePackage[english, czech]{babel}
\fi
\endinput
Here is a MWE using that package:

\documentclass{article}
%\usepackage{yourpackagename} % comment one of those two lines
\usepackage[en]{yourpackagename}
\begin{document}
% --- sanity check ---
The \texttt{babel} options were loaded in the following order:
\makeatletter
\ifyourpkgprefix@enoption%
\texttt{czech, english} (option~\texttt{en} was passed).
\else%
\texttt{english, czech} (option~\texttt{en} was NOT passed).
\fi
\makeatother
% --------------------
foobar
\end{document}
Useful resources: