Start by designing the hardware, it isn't complicated, think of the things you need such as the displays themselves and switches to set the time. Decide whether you are going to use LCD or LED displays and how many switches you need. From there, work out how many connections you need back to the microcontoller. Remember that LCD displays usually use 4 data lines and some control signals but you have to prepare the data in software before sending it to the display. LED displays are usually multiplexed, meaning the same segment in each digit is linked together to save on connections but only one digit at a time is actually lit, they are sequenced so fast that human eyes perceive them as being on all the time.
When you have worked out the hardware you can see which resources are needed in the microcontroller and from there decide how to structure the program. You then choose the processor and language you want to use to write the program. While doing all this, think carefully about what the clock is supposed to do, for example, should it remember the time and keep running when the power is turned off and how accurate does it have to be.
Brian.