On the ATmega, the I2C pins are alternative functions of the Analog pins. Port C5 is the Clock (SCL) and C4 is Data (SDA). You can set the internal pull-ups in the ATmega or use external ones. (prob. best to use external ones)
You do not need to add pull-up resistors as they are already present.
Just a warning for further development: There is know bug in the BCM2835 I2C interface.
The clock stretching is a bit terribly broken so you have the be very careful what you are doing.
I have a program running on the ATmega. I see no errors provided:
1/ I use a 100KHz I2C clock.
2/ My Atmega interrupt routine is extremely efficient.
I still have to test what happens if multiple interrupts occur at the same time as I don't know
what the Amega interrupt priority is.