Here is my code:
\documentclass[letterpaper,10pt,fleqn]{article}
\setlength{\mathindent}{1cm}
\usepackage{geometry}
\geometry{textheight=9in, textwidth=6.5in}
\usepackage{amssymb}
\usepackage{amsmath}
\numberwithin{equation}{section}
\parindent = 0.0in
\parskip = 0.2in
\begin{document}
\section*{New Section}
\hrule
Text
\begin{align}
\phi =& \int_S \mathrm{d}a\\
=& \int_S f(u, v) |\mathbf{T}_u \times \mathbf{T}_v| \mathrm{d}u\mathrm{d}v
\end{align}
\end{document}
I don't want the number to be in front of "New Section", so I am using the asterisk \section*{New Section} but I do want the equations to be numbered as (1.1) and (1.2) etc. However, I have found that using the asterisk sets the equation numbers to (0.1) and (0.2) and I have yet to find a way around this.
\numberwithininstruction which doesn't make sense. – egreg Oct 09 '13 at 21:29