Hi, denyan.
Seems simple enough. Get the DS1307 data sheet. Use the Atom's I2C commands to set the 1307's registers to produce the 1Hz output. Connect that to one of the interrupt-on-change pins and use the EXTINT command to work with it.
There is an app note under the Atom's Download section about using the DS1302. This is a SPI part with no squarewave output, but it will get you started.
Remember, keep the clock crystal real close to the part or expect trouble.
Also, do a search on the web. This should be a common project.
Basic Micro is now ready to update and upgrade their examples and app notes. In the future, ask for code examples of interest to you in the "Wish List" forum. Be sure to state which product you're using and what, if anything, you want to interface to. Give a time frame (immediate, in 30 days, 60 days). The answers may be anything from generic to specific. As always, my job is to advise and guide, not provide complete and bulletproof solutions. I am supposed to receive (literally) one of every product so I can answer questions intelligently here, with real world test and experience, and start producing code examples. Mind you, I don't have these items yet, and may not have them all for a month or so.
Take care,
kenjj