Both 1.0 and the nightly should just use whichever file it is that you provide them. I don't believe the engine needs to be upgraded to be patched but the upgraded game from the nightly might well already have the patch, or not, since it too will read whichever map you provide it.
Regardless, it is a good thing to upgrade from 1.0 to the nightly. As volutar said, it is a bit old now..
(If you need help, feel free to send me a pm, I also run on Ubuntu and I have notes on how I install nightlies)