One of the better books I've found is Arduino Internals by Dale Wheat. This is an in-depth look at bypassing most of the Arduino shell and getting down to bare metal. As for the DS1307, it's just an I2C peripheral. You can't get 'down to the chip' unless you remove it from the component board it currently is soldered to. You certainly can however, talk to it through SDA and SCL without the use of a library, just learn its language. As John said, get the datasheet. Get datasheets on everything, they rarely change.