You can number each line using the alignat environment from the amsmath package.
\documentclass{article} \usepackage{amsmath} \begin{document} \begin{alignat}{2} a &= b &\quad\Rightarrow\quad c &= d \\ e &= f & g &= h \end{alignat} \end{document} 
You can use \nonumber to suppress numbering on individual lines. I don't think it would be a good idea to separately number the equations in the left-hand column. Readers expecting to find the equation numbers at the edge of the page are likely to find this annoying.
