Equation numbering
Simple equation
To give an equation a number, use the \tag{}. To refer to it later, use \label{} to label this equation. When you want to refer to it, use \eqref{}. For example,
$$e=mc^2 \tag{1}\label{eq1}$$
Equation $\eqref{eq1}$ is one of the greatest equations in mankind's history. Equation $\eqref{eq1}$ is produced using the following code,
$$e=mc^2 \tag{1}\label{eq1}$$ To refer to it, use \eqref{eq1}.
Multi-line equation
Multi-line equation is actually just one equation rather than several equations. So the correct environment is aligned instead of align.
$$\begin{equation}\begin{aligned} a &= b + c \\ &= d + e + f + g \\ &= h + i \end{aligned}\end{equation}\tag{2}\label{eq2}$$
Equation $\eqref{eq2}$ is a multi-line equation. The code to produce equation $\eqref{eq2}$ is
$$\begin{equation}\begin{aligned} a &= b + c \\ &= d + e + f + g \\ &= h + i \end{aligned}\end{equation}\tag{2}\label{eq2}$$ Multiple aligned equations
For multiple aligned equations, we use the align environment.
$$\begin{align} a &= b + c \tag{3}\label{eq3} \\ x &= yz \tag{4}\label{eq4}\\ l &= m - n \tag{5}\label{eq5} \end{align}$$
Equation $\eqref{eq3}$, $\eqref{eq4}$ and $\eqref{eq5}$ are multiple equations aligned together. The code to produce these equations is,
$$\begin{align} a &= b + c \tag{3}\label{eq3} \\ x &= yz \tag{4}\label{eq4}\\ l &= m - n \tag{5}\label{eq5} \end{align}$$