And it even plays the startup video now as where it didn't before with the plug and play modules enabled.
by default, the video is not enabled in plugnplay mode, but it is possible to have it.
Now am I assuming correctly that if I want to edit the layout and options that I would only edit the daphne.cfg
Yes, correct, you have to work only on your Daphne.cfg , the Atomic019.cfg file is not used anymore (anyway it was not used in Plugnplay mode).
One thing I still need to configure is exiting games....... meaning generally ya use the ESC key to quit a Daphne game, but if someone hits it again for whatever reason it will close the frontend. Should I just map a different key for exiting one or the other?
you have 2 options with Atomic :
-you can change the exit key of Atomic , using AtomicKey.exe
-Or you can put a Password on exit (password can be entered using the controlpanel) , it is an option of Atomic. If the correct password is not entered after few second, it go back to the fe screen.
A 3rd options would be to change the exit key of Daphnee , but i don't know if it is possible.