SPI hookup to ATmega644
You can't use SPI for just any three-wire interface. In SPI there's no separate reading vs writing mode. Bits get exchanged in both directions at every clock, so you really need a separate wire to MISO if you need bidirectional communication.

In this case, I would argue that it will work even though you're using the same pins for your ISP port. However, in your code you won't be able to use the hardware SPI interface. 

That is fine, though. You'll have to bit-bang communication with the DS1302, but speed is not critical for this application, is my guess.