What on Earth are you trying to achieve by this?
For a start the drivers for your devices will need to install to the Windows System direcory and not all programs will work if they are not installed on the system disc with Windows.
Why the need for two versions of Windows Me? One was too much trouble for me,lol......better off just upgrading to XP if you ask me.
If you have some older programs that wont run with XP then dual booting with one version of Me on a single partition or the second drive is ok.But you are far better off keeping all the Windows/drivers/programs on the one partition.