align the '=' in separate equations always at the center of the page

Use the \intertext command of the amsmath package. As a side-note, use \mathrm instead of \rm. Moreover, it's usually better not to clutter the code with unnecessary braces, since it becomes harder to understand. Finally, \left-\right is only needed when enclosing terms of unusual height in parentheses.

\documentclass{article}
\usepackage{amsmath}
\usepackage{siunitx}
\begin{document}
some text ...
\begin{align}
  \mathrm{SE} 
   &= \sqrt{\frac{\sum\nolimits_{i = 1}^n {(x_i-\bar x)}^2 }%
                 {n \cdot (n-1)}
           }                                               \label{eqn:SE} \\
   &=  \frac{\mathrm{SD}}{\sqrt n}                         \label{eqn:SE2}\\
\intertext{some text ...}
  \mathrm{RSE}
   &= \frac{\mathrm{SEM}}{\bar x} \cdot \SI{100}{\percent} \label{eqn:SEM}
\end{align}
\end{document}

If you really want the equals sign centered, you might try defining an environment like

\newenvironment{calign}
  {\align\hspace{.5\textwidth} &\hspace{.5\textwidth}\notag\\[-2em]}
  {\endalign}

Then you can replace all of your aligns with caligns to ensure that the equals sign is always in the same place. (Here it is actually the left end of the = which is centered. It doesn't make a huge difference to the layout, and you could probably fix it using the calc package if you need to.)

This is probably not a particularly robust solution and might need to be adjusted, e.g., if you have changed the vertical spacing in align environments. It will also break if the LHS of the equation doesn't fit in the allotted space, in which case it will push the tag numbers off the edge (but for this case you can still revert to the original align environment.)

You can do a similar but slightly more complicated thing if you need a starred version as well.