The REVTeX macro package allows two methods for numbering equations: you can assign your own equation numbers or you can allow REVTeX to number for you.
Use the command \eqnum{#1} to number your own equations. You can
also use this command to produce a specific equation number not normally
obtainable; 
, for example. Numbers assigned by \eqnum{#1} are
completely independent of the automatic numbering.
For automatically numbered single-line and multiline equations, use the
equation and eqnarray environments. You can use the
\[,\] commands and the eqnarray
environment for
unnumbered single-line and multiline equations, respectively. The command
\nonumber will suppress the numbering on a single line of an
eqnarray.
If you wish a series of equations to be a lettered sequence, e.g., (3a), (3b), and (3c), just include the equation(s) or eqnarray(s) within the mathletters environment.
Finally, to have REVTeX number equations by section, use the eqsecnum style option.
See apssamp.tex to see examples of how all this works.