The automation is currently not part of ctable, since numbering is done using an optional argument to both \tnote[<num>] and \tmark[<num>].
Based on your (very) minimal example, the following should suffice:

\documentclass{article}
\usepackage{ctable}% http://ctan.org/pkg/ctable
\usepackage{etoolbox}% http://ctan.org/pkg/etoolbox
\newcounter{ctabfnote}\newcounter{ctabfmark}
\renewcommand{\thectabfnote}{\alph{ctabfnote}}
\renewcommand{\thectabfmark}{\alph{ctabfmark}}
\pretocmd{\ctable}% <cmd>
{\setcounter{ctabfnote}{0}%
\setcounter{ctabfmark}{0}}% <prepend>
{}{}% <success><failure>
\makeatletter
\renewcommand{\tnote}[1]{%
\stepcounter{ctabfnote}%
\ifx\@ctblnotespar\@ctbltrue%
\@ctbltextsuperscript{\normalfont\textit{\thectabfnote}}\,#1
\else%
\hbox{\@ctbltextsuperscript{\normalfont\textit{\thectabfnote}}}\NN
\fi
}
\renewcommand{\tmark}{%
\stepcounter{ctabfmark}%
\hbox{\textsuperscript{\normalfont\textit{\thectabfmark}}}}
\makeatother
\begin{document}
\ctable[
] {rl} {
\tnote{first footnote}
\tnote{second footnote}
}{
\FL Configuration & Error
\ML Full\tmark & 0.0
\ML Partial\tmark & 0.0
\LL
}
\end{document}
Two new counters are introduced, one for each of \tnote and \tmark. I've also modified the input to \tnote and \tmark to drop the optional argument, since they're not needed anymore. Counter are reset at the start of \ctable (via a patch thanks to etoolbox).