Hey Stephen,
Eclipse manages its own config in the <eclipsedir>/.config directory. I had a quick look but I don't think you're supposed to edit the files there by hand
Aside from creating a shortcut/batch file that passes appropriate options, I dunno what to do from here....Eclipse seems to be a bit like that. I don't know of anywhere you explicitly set the JVM etc. That said I don't pass any command line args explicitly, so maybe there are defaults that work in most situations.
Sorry I couldn't help more
--Tim