With pandoc 1.12.x and it’s new YAML metadata capabilities you could add all the information and all LaTeX-code you need in your markdown document like this:

---
title: Test
author: Author Name
header-includes: |
    usepackage{fancyhdr}
    pagestyle{fancy}
    fancyhead[CO,CE]{This is fancy}
    fancyfoot[CO,CE]{So is this}
    fancyfoot[LE,RO]{thepage}
abstract: This is a pandoc test . . . 
...

# This is a test

Lorem ipsum....

That way you don't have to modify the template, simply calling pandoc doc.md -o doc.pdf will suffice.

---

If you want more control, you can add new metadata like this:

---
title: Test
author: Author Name
header: This is fancy
footer: So is this
geometry: margin=1in
abstract: This is a pandoc test . . . 
...

# This is a test

Lorem ipsum....

To make this work, you have to modify the template (pandoc -D latex > template.latex) accordingly:

% filename: template.latex

documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$lang$,$endif$$if(papersize)$$papersize$,$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$}
usepackage[T1]{fontenc}

% -----------------------
% Using abstracts
usepackage{abstract}

% -----------------------
% Using fancy headers and footers
usepackage{fancyhdr}
pagestyle{fancy}
fancyhead[CO,CE]{$header$}
fancyfoot[CO,CE]{$footer$}
fancyfoot[LE,RO]{thepage}

usepackage{lmodern}
usepackage{amssymb,amsmath}
usepackage{ifxetex,ifluatex}
usepackage{fixltx2e} % provides textsubscript
% use upquote if available, for straight quotes in verbatim environments
IfFileExists{upquote.sty}{usepackage{upquote}}{}
ifnum 0ifxetex 1fiifluatex 1fi=0 % if pdftex
  usepackage[utf8]{inputenc}
$if(euro)$
  usepackage{eurosym}
$endif$
else % if luatex or xelatex
  ifxetex
    usepackage{mathspec}
    usepackage{xltxtra,xunicode}
  else
    usepackage{fontspec}
  fi
  defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
  newcommand{euro}{€}
$if(mainfont)$
    setmainfont{$mainfont$}
$endif$
$if(sansfont)$
    setsansfont{$sansfont$}
$endif$
$if(monofont)$
    setmonofont[Mapping=tex-ansi]{$monofont$}
$endif$
$if(mathfont)$
    setmathfont(Digits,Latin,Greek){$mathfont$}
$endif$
fi
% use microtype if available
IfFileExists{microtype.sty}{usepackage{microtype}}{}
$if(geometry)$
usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
$endif$
$if(natbib)$
usepackage{natbib}
bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
$endif$
$if(biblatex)$
usepackage{biblatex}
$if(biblio-files)$
bibliography{$biblio-files$}
$endif$
$endif$
$if(listings)$
usepackage{listings}
$endif$
$if(lhs)$
lstnewenvironment{code}{lstset{language=Haskell,basicstyle=smallttfamily}}{}
$endif$
$if(highlighting-macros)$
$highlighting-macros$
$endif$
$if(verbatim-in-note)$
usepackage{fancyvrb}
$endif$
$if(tables)$
usepackage{longtable}
$endif$
$if(graphics)$
usepackage{graphicx}
% Redefine includegraphics so that, unless explicit options are
% given, the image width will not exceed the width of the page.
% Images get their normal width if they fit onto the page, but
% are scaled down if they would overflow the margins.
makeatletter
defScaleIfNeeded{%
  ifdimGin@nat@width>linewidth
    linewidth
  else
    Gin@nat@width
  fi
}
makeatother
letOldincludegraphicsincludegraphics
{%
 catcode`@=11relax%
 gdefincludegraphics{@ifnextchar[{Oldincludegraphics}{Oldincludegraphics[width=ScaleIfNeeded]}}%
}%
$endif$
ifxetex
  usepackage[setpagesize=false, % page size defined by xetex
              unicode=false, % unicode breaks when used with xetex
              xetex]{hyperref}
else
  usepackage[unicode=true]{hyperref}
fi
hypersetup{breaklinks=true,
            bookmarks=true,
            pdfauthor={$author-meta$},
            pdftitle={$title-meta$},
            colorlinks=true,
            citecolor=$if(citecolor)$$citecolor$$else$blue$endif$,
            urlcolor=$if(urlcolor)$$urlcolor$$else$blue$endif$,
            linkcolor=$if(linkcolor)$$linkcolor$$else$magenta$endif$,
            pdfborder={0 0 0}}
urlstyle{same}  % don't use monospace font for urls
$if(links-as-notes)$
% Make links footnotes instead of hotlinks:
renewcommand{href}[2]{#2footnote{url{#1}}}
$endif$
$if(strikeout)$
usepackage[normalem]{ulem}
% avoid problems with sout in headers with hyperref:
pdfstringdefDisableCommands{renewcommand{sout}{}}
$endif$
setlength{parindent}{0pt}
setlength{parskip}{6pt plus 2pt minus 1pt}
setlength{emergencystretch}{3em}  % prevent overfull lines
$if(numbersections)$
setcounter{secnumdepth}{5}
$else$
setcounter{secnumdepth}{0}
$endif$
$if(verbatim-in-note)$
VerbatimFootnotes % allows verbatim text in footnotes
$endif$
$if(lang)$
ifxetex
  usepackage{polyglossia}
  setmainlanguage{$mainlang$}
else
  usepackage[$lang$]{babel}
fi
$endif$
$for(header-includes)$
$header-includes$
$endfor$

$if(title)$
title{$title$}
$endif$
$if(subtitle)$
subtitle{$subtitle$}
$endif$
author{$for(author)$$author$$sep$ and $endfor$}
date{$date$}

begin{document}
$if(title)$
maketitle
$endif$

$for(include-before)$
$include-before$

$endfor$
$if(toc)$
{
hypersetup{linkcolor=black}
setcounter{tocdepth}{$toc-depth$}
tableofcontents
}
$endif$
%-----------------------------------
% Adding the abstract

$if(abstract)$
begin{abstract}
$abstract$
end{abstract}
$endif$

$body$

$if(natbib)$
$if(biblio-files)$
$if(biblio-title)$
$if(book-class)$
renewcommandbibname{$biblio-title$}
$else$
renewcommandrefname{$biblio-title$}
$endif$
$endif$
bibliography{$biblio-files$}

$endif$
$endif$
$if(biblatex)$
printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$

$endif$
$for(include-after)$
$include-after$

$endfor$
end{document}

This is also the place to create a title page. As you can see, the template is nothing but a LaTeX document with some $variables$, so it should be easy to customize to your liking.

Now just call pandoc with the template option:

pandoc -s -N --template=template.latex doc.md -o doc.pdf

You can find the documentation for templates here: https://pandoc.org/MANUAL.html#templates