As I work more with this, I have found that the SDL joystick interferes with the keyboard (well DUH!) so, if you wish to use it as an 8bit computer and not a Game System you need to add

SDL_JOY_0_ENABLED=0

to the end of the /home/user/.atari800.cfg

and then comment it out or remove it when you want to use the d-pad as a joystick. alternately, I could remove the codings for the SDL_Joy_0 from the code and put it all in the config, but either way you would still have to change something to use the keyboard or the joystick as I have it set up now. you can add the lines:
SDL_JOY_0_ENABLED=1
SDL_JOY_0_LEFT=260
SDL_JOY_0_RIGHT=262
SDL_JOY_0_UP=264
SDL_JOY_0_DOWN=258
SDL_JOY_0_LEFTUP=263
SDL_JOY_0_RIGHTUP=265
SDL_JOY_0_LEFTDOWN=257
SDL_JOY_0_RIGHTDOWN=259
SDL_JOY_0_TRIGGER=306
SDL_JOY_1_ENABLED=0
SDL_JOY_1_LEFT=97
SDL_JOY_1_RIGHT=100
SDL_JOY_1_UP=119
SDL_JOY_1_DOWN=120
SDL_JOY_1_LEFTUP=113
SDL_JOY_1_RIGHTUP=101
SDL_JOY_1_LEFTDOWN=122
SDL_JOY_1_RIGHTDOWN=99
SDL_JOY_1_TRIGGER=9

to /home/user/.atari800.cfg and change the mappings to be whatever you want using the SDL code for whichever buttons you want.
http://www.libsdl.org/cgi/docwiki.cgi/SDLKey

Personally I hate trying to use one of the top buttons as fire when using the dpad as the movement so I have it mapped to the center button, but that being enter/return can cause problems hence the config to change it...
Attached is the latest version with the FULLSCREEN toggle working properly on the (ironically enough) Fullscreen button.

-John