yes, as kubeek says, you can hook them to any pins you want. The difference is, the software necessary. If you don't use the spi port on the ATMEGA, then you have to 'bit bang' the serial data transfer. If you use the spi port, you can just send data through the serial registers and implement the interrupt features.
I'm a little confused.
The DS1307 Chip has an I²C Interface?!
So the pins should be conected to the TWI Pins SDA SCL.
SPI normally uses the Pins MISO MOSI and SCK and !CE.
I would suggest you to use the TWI hardware interface.
It works faster and is easier to use than a software solution.
Thanks, i was just curious about it, all sites i saw it was connected to SDA and SCL but noone really explained why it was like that, and what would be required to connect it elsewhere.