thanks for tip, been struggling with the atari 5200 and 800 roms but managed to find a way to also run the 800 roms on the 5200 emulator. Here's my .atari800.cfg which is placed into the bios folder.
Also the 5200 rom should be named 5200.rom (lower case .rom)
Atari 800 Emulator, Version 3.1.0
ROM_OS_A_NTSC=
ROM_OS_A_PAL=ATARIOSA.ROM
ROM_OS_B_NTSC=
ROM_OS_AA00R10=
ROM_OS_AA00R11=
ROM_OS_BB00R1=
ROM_OS_BB01R2=ATARIXL.ROM
ROM_OS_BB02R3=
ROM_OS_BB02R3V4=
ROM_OS_CC01R4=
ROM_OS_BB01R3=
ROM_OS_BB01R4=
ROM_OS_BB01R59=
ROM_OS_BB01R59A=
ROM_5200=5200.rom
ROM_5200_A=
ROM_BASIC_A=
ROM_BASIC_B=
ROM_BASIC_C=ATARIBAS.ROM
ROM_XEGAME=
ROM_400/800_CUSTOM=ATARIOSB.ROM
ROM_XL/XE_CUSTOM=
ROM_5200_CUSTOM=
ROM_BASIC_CUSTOM=
ROM_XEGAME_CUSTOM=
OS_400/800_VERSION=AUTO
OS_XL/XE_VERSION=AUTO
OS_5200_VERSION=AUTO
BASIC_VERSION=AUTO
XEGS_GAME_VERSION=AUTO
H1_DIR=
H2_DIR=
H3_DIR=
H4_DIR=
HD_READ_ONLY=1
PRINT_COMMAND=lpr %s
SCREEN_REFRESH_RATIO=1
MACHINE_TYPE=Atari XL/XE
RAM_SIZE=64
DEFAULT_TV_MODE=PAL
MOSAIC_RAM_NUM_BANKS=0
AXLON_RAM_NUM_BANKS=0
ENABLE_MAPRAM=0
DISABLE_BASIC=1
ENABLE_SIO_PATCH=1
ENABLE_H_PATCH=1
ENABLE_P_PATCH=1
ENABLE_NEW_POKEY=1
STEREO_POKEY=0
SPEAKER_SOUND=1
BUILTIN_BASIC=0
KEYBOARD_LEDS=0
F_KEYS=0
BUILTIN_GAME=0
KEYBOARD_DETACHED=0
1200XL_JUMPER=0
CFG_SAVE_ON_EXIT=1
MIO_ROM=
BLACK_BOX_ROM=
XLD_D_ROM=
XLD_V_ROM=
CARTRIDGE_FILENAME=
CARTRIDGE_TYPE=0
CARTRIDGE_PIGGYBACK_FILENAME=
CARTRIDGE_PIGGYBACK_TYPE=0
CARTRIDGE_AUTOREBOOT=1
CASSETTE_FILENAME=
CASSETTE_LOADED=0
CASSETTE_WRITE_PROTECT=0
RTIME=1
COLOURS_NTSC_SATURATION=0
COLOURS_NTSC_CONTRAST=0
COLOURS_NTSC_BRIGHTNESS=0
COLOURS_NTSC_GAMMA=0.3
COLOURS_NTSC_HUE=0
COLOURS_NTSC_GTIA_DELAY=26.8
COLOURS_NTSC_EXTERNAL_PALETTE=
COLOURS_NTSC_EXTERNAL_PALETTE_LOADED=0
COLOURS_NTSC_ADJUST_EXTERNAL_PALETTE=0
COLOURS_PAL_SATURATION=0
COLOURS_PAL_CONTRAST=0
COLOURS_PAL_BRIGHTNESS=0
COLOURS_PAL_GAMMA=0.3
COLOURS_PAL_HUE=0
COLOURS_PAL_GTIA_DELAY=23.2
COLOURS_PAL_EXTERNAL_PALETTE=
COLOURS_PAL_EXTERNAL_PALETTE_LOADED=0
COLOURS_PAL_ADJUST_EXTERNAL_PALETTE=0
ARTIFACT_NTSC=NONE
ARTIFACT_PAL=NONE
ARTIFACT_NTSC_MODE=0
SCREEN_SHOW_SPEED=0
SCREEN_SHOW_IO_ACTIVITY=1
SCREEN_SHOW_IO_COUNTER=0
SCREEN_SHOW_1200XL_LEDS=1
SOUND_ENABLED=1
SOUND_RATE=44100
SOUND_BITS=16
SOUND_FRAG_FRAMES=0
SOUND_LATENCY=20
VIDEO_FILTERING=1
VIDEO_ZOOM=1.00
SDL_JOY_0_ENABLED=1
SDL_JOY_0_LEFT=260
SDL_JOY_0_RIGHT=262
SDL_JOY_0_UP=264
SDL_JOY_0_DOWN=261
SDL_JOY_0_TRIGGER=305
SDL_JOY_1_ENABLED=0
SDL_JOY_1_LEFT=97
SDL_JOY_1_RIGHT=100
SDL_JOY_1_UP=119
SDL_JOY_1_DOWN=115
SDL_JOY_1_TRIGGER=306