You probably should look into the ledmac and ledpar packages http://www.djdekker.net/ledmac/
As far as I know LyX does not support these packages from the GUI, however you may be content to use ERT to insert raw LaTeX, but it is also possible that this is easier to do in a good LaTeX editor... If you really want to use LyX you could probably make an module or an layout for ledpar, however this may be a bit tricky. If you you like a challenge have a look in Customizing in the Help menu in LyX. Ingar
