It's never a good idea to modify directly a .sty file; that said, classicthesis uses the titlesec package to format the sectional unit headings and, in particular, it uses
\titlespacing*{\chapter}{0pt}{1\baselineskip}{1.2\baselineskip}
to control the space before and after chapter titles, so you can simply change the third (space after) and fourth (space after) arguments according to your needs; you can do this in the preamble of your document without changing classicthesis.sty. A simple example:
\documentclass[11pt,a5paper,footinclude=true,headinclude=true]{scrbook}
\usepackage[linedheaders,parts,pdfspacing]{classicthesis} % ,manychapters
\usepackage{lipsum}
\titlespacing*{\chapter}{0pt}{*12}{*7}
\begin{document}
\tableofcontents
\chapter{Test Chapter One}
\section{A Section}
\lipsum[1-6]
\chapter{Test Chapter One}
\lipsum[1]
\section{A Section}
\lipsum[1]
\end{document}
Of course, instead of the values I used (refer to the documentation for titlesec) you can use any valid length.

If the changes in spacing must apply only to numbered chapters, instead of using \titlespacing, a solution using \titleformat to discriminate between numbered and unnumbered chapters (with the help of the numberless key) can be used; in the following code I illustrate this approach in the case of the lineheaders option; for numbered chapters a space of 8\baselineskip was added before the title and 2\baselineskip was added after the tile; unnumbered chapters maintain their original settings:
\documentclass[11pt,a5paper,footinclude=true,headinclude=true]{scrbook}
\usepackage[linedheaders,parts,pdfspacing]{classicthesis} % ,manychapters
\usepackage{lipsum}
\titleformat{\chapter}[display]%
{\vspace*{8\baselineskip}}{\raggedleft{\color{halfgray}\chapterNumber\thechapter} \\ }
{0pt}{\titlerule\vspace*{.9\baselineskip}\raggedright\spacedallcaps}
[\normalsize\vspace*{.8\baselineskip}\titlerule\vspace*{2\baselineskip}]
\titleformat{name=\chapter,numberless}[display]%
{\relax}{}
{0pt}{\titlerule\vspace*{.9\baselineskip}\raggedright\spacedallcaps}
[\normalsize\vspace*{.8\baselineskip}\titlerule]
\begin{document}
\tableofcontents
\chapter{Test Chapter One}
\section{A Section}
\lipsum[1-6]
\chapter{Test Chapter One}
\lipsum[1]
\section{A Section}
\lipsum[1]
\end{document}