While Minwah is right, I found that it's actually no that bad to port over, for example the layout files just need to be renamed with the new convention (emu1-main.jog becomes mame-main.jpg for example) but you shouldn't have to change the contents of your .lay file.
If your lists were generated using catver filters, you should be able to re-create them easily. If you had manually added or deleted games to the list however, you might have to do that again.
So if there are new featurs you really want, it's probably worth the effort to chnage the configuration over,