in your .atari800.cfg file
namely this settings adjust video sizing within the file (or access via F1 in game, adjust , and save settings):
VIDEOMODE_WINDOW_WIDTH=336
VIDEOMODE_WINDOW_HEIGHT=240
VIDEOMODE_FULLSCREEN_WIDTH=1920
VIDEOMODE_FULLSCREEN_HEIGHT=1080
VIDEOMODE_WINDOWED=0
VIDEOMODE_HORIZONTAL_AREA=TV
VIDEOMODE_VERTICAL_AREA=TV
VIDEOMODE_HORIZONTAL_SHIFT=0
VIDEOMODE_VERTICAL_SHIFT=0
VIDEOMODE_STRETCH=FULL
VIDEOMODE_FIT=BOTH
VIDEOMODE_IMAGE_ASPECT=REAL
VIDEOMODE_ROTATE90=0
VIDEOMODE_HOST_ASPECT_RATIO=64:27
VIDEOMODE_80_COLUMN=1
or you can use command line entries as documented in the DOC folder in the USAGE.txt file. For example fullscreen command is:
Best to stick to one way or the other (CFG file or command lines) just to avoid confusion.
As far as controllers, yes it will work with controllers out of box; however, only as far as what the game supports for a "real" Atari 800. I don't be believe Atari 800 (the emulator) has input mapping to controller natively (it didn't use to which is why my default is Altirra). Thus, you will have to hit F4 on some games to start (Asteroids as example) or use an external mapping program to map a keyboard to controller button. Altirra has a mapping interface within the emulator that you can tell it to map the Atari 800 START button to a controller button.