Subequations allow to be referred either each item individually e.g. (12a), or as a whole using the common number (12):
\begin{subequations}
\label{eq12}
\begin{align}& \begin{aligned}
\ddot{\xi}+\frac{1}{2r^2}\xi\frac{\dd^2}{\dd t^2}(\xi^2+&\zeta^2) +2\beta_{\xi}\dot{\xi}+ \\
& +\omega_0^2\xi
\left(1+\frac{1}{2r^2}(\xi^2+\zeta^2)\right) =-\ddot{a}
\end{aligned}
\label{eq12a}
\\[3mm]
&\begin{aligned}
\ddot{\zeta}+\frac{1}{2r^2}\zeta\frac{\dd^2}{\dd t^2}(\xi^2+&\zeta^2) + 2\beta_{\zeta}\dot{\zeta}+
\\& + \omega_0^2\zeta
\left(1+\frac{1}{2r^2}(\xi^2+\zeta^2)\right) = 0
\end{aligned}
\label{eq12b}
\end{align}
\end{subequations}
the system (\ref{eq12}) is analyzed ... but the first equation (\ref{eq12a}) ...
