In order to start programming ClockTHREE without any boards on hand, I built up a small column of LEDs with the ClockTWO schematic.
On the left most section of breadboard, you can see the FTDI interface (5 pins in the upper left) and the column driver. The column driver has 16 output pins, one for each column of the array, and 4 input pins. Only one output pin is active at a time. If all four input pins are set at low voltage (ground) LLLL, the first output pin is made active. LLLH activates the second output pin, LLHL, the third and so on counting in binary up to 15 which activates the 16th output pin. So this chip is used to sequentially activate each column.
The row driver is on the right. This chip is both a serial to parallel converter and a current limiter. The inputs are ground v+, clock, and data. The data line accepts a sequence of 16 low and high values that indicate which output pins should be low or high. So to light only the first LED in white the value LLLLLLLLLLLLLHHH is sent over the data line in 16 clock cycles. It takes three H values to make white since Red + Green + Blue = white. Both ClockTWO and ClockTHREE require two of these row drivers for a total of 32 (3 x10 RGB + 2 Mono) outputs.
In the center you can see the ATMega328 controler IC. This is the brains of the operation. It sends the data for the current column to the row driver then activates the column with the column driver before moving to the next column.
The auxiliary breadboard on the right contains the top 4 LEDs on a single column. For the first time I could see how bright the array will be and to check flicker. The LEDs emit mellow colors without flicker. Whew!
I used the LEDs on the top to debug the column logic. I've used this RadioShack board I received as a gift for a lot of different projects. Its super handy, but kind of expensive; I probably would have never bought it for myself. But, to learn electronics on, you can't beat it. I love the included hand written manuals by Forest Mims. The digital circuits manual is available online.