Hi,
I would not use abbreviations such as \be and \ee for beginning and ending equations: you hide the real meaning, you use commands instead environment syntax. Who should understand in the first post, what those abbreviations mean? Your second post at least shows the definitions.
Back to your equation: you wrote one equation, so you get one number only. Within the equation you used an array, LaTeX cannot know that you would like to number rows of an array. Smaller size is a result of your \newcommand\be{\begin{equation}\footnotesize}.
Here's how you could do it, using align:
Code: Select all
\begin{align}
\frac{d\mathbf{V}_f}{dt}&= - \frac{C_{Daf} S_f \rho \mathbf{V}_f^2}{2 m_f}-g\sin\gamma_f\\
\frac{d \gamma_f}{dt}&=\frac{1}{\mathbf{V}_f} \left( \frac{C_{Laf}S_f\rho\mathbf{V}_{f}^2}{2m_f} -g\cos\gamma_f \right) \\
\frac{dx}{dt}&=V_f\cos\gamma_f \\
\frac{dz}{dt}&=V_f\sin\gamma_f\\
\frac{d x_1}{dt}&=V_s-V_f\cos\gamma_f\\
\frac{d\theta_f}{dt}&=\omega_{yf}\\
\frac{d\omega_{yf}}{dt}&=\frac{C_{mf}S_f l_f \rho \mathbf{V}_f^2}{2I_{yf}}\\
\alpha_f&=\theta_f-\gamma_f
\end{align}
Note, & marks the equal signs for alignment.
Have a look at
mathmode.pdf for learning about writing maths with LaTeX. Since you write a scientific document, I guess reading this is easy for you.
Stefan