Can I use an Arduino uno with an atmega chip together?

I want to make a really simple handheld console with 2 matrix displays, one buzzer, two buttons and one joystick. I want to use the Arduino Uno chip as the bios of the system. The bios will initialize the SD card slot, check if an SD card is there, check if there is any game on it and let the user choose the game he wants to play. Then when the user chooses the game (which is a compiled Arduino sketch as a hex file) the bios chip will program the other chip. The other chip is going to be the same atmega chip as the Arduino uno.

Is it possible for the other chip to take over the bios chip?

Yes, this is possible. In fact, the Arduino Uno R3 already uses two ATmega chips: one to act as a USB interface that programs the other.

But the device you describe is not "really simple" and will require advanced programming skills.

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Maybe it can be something like you are looking for:

Actually the UNO programs itself using the bootloader.

Google "Everything You Always Wanted to know about Arduino Bootloading but Were Afraid to Ask Bald Wisdom"

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