Lol, lot of problems, I can't answer for resolution problem but :
Yep there is a "save button", but you can configure the frontend on your "first computer" and copy the file on the "arcade box" with the lower resolution, I make like this too because my "arcade box" havent keyboard on it.
Keys are configurables too in Runaway. And there is some modification since the 4.0 version.
For the rom name problem, check the option "use datafile" on RunAway and of course make the database.