Frankfurt uses the smoothbars outer theme which sets the headline template but doesn't set the footline template. To change the header position to the bottom of the frame, it's enough to set the footline template to behave exactly as smoothbars sets the headline template. To place the navigation symbols in the header, you need to redefine the navigation symbols template to do nothing and then to insert the symbols in the headline template:
\documentclass{beamer}
\usetheme{Frankfurt}
\setbeamertemplate{navigation symbols}{}
\makeatletter
\setbeamertemplate{footline}
{%
\pgfuseshading{beamer@barshade}%
\ifbeamer@sb@subsection%
\vskip-9.75ex%
\else%
\vskip-7ex%
\fi%
\begin{beamercolorbox}[ignorebg,ht=2.25ex,dp=3.75ex]{section in head/foot}
\insertnavigation{\paperwidth}
\end{beamercolorbox}%
\ifbeamer@sb@subsection%
\begin{beamercolorbox}[ignorebg,ht=2.125ex,dp=1.125ex,%
leftskip=.3cm,rightskip=.3cm plus1fil]{subsection in head/foot}
\usebeamerfont{subsection in head/foot}\insertsubsectionhead
\end{beamercolorbox}%
\fi%
}%
\setbeamertemplate{headline}{%
\hskip1em\usebeamercolor[fg]{navigation symbols dimmed}%
\insertslidenavigationsymbol%
\insertframenavigationsymbol%
\insertsectionnavigationsymbol%
\insertsubsectionnavigationsymbol%
\insertdocnavigationsymbol%
\insertbackfindforwardnavigationsymbol%
}
\makeatother
\begin{document}
\section{Test section}
\subsection{Test subsection one}
\begin{frame}Test\end{frame}
\subsection{Test subsection two}
\begin{frame}Test\end{frame}
\end{document}

Frankfurtalone doesn't produce any footer, since it uses thesmoothbarsouter theme which sets theheadlinetemplate but doesn't set thefootlinetemplate. How are you producing the footer? – Gonzalo Medina Nov 21 '11 at 16:32