Ok, I have finally read all the relevant information about 4101 drivers to ask some questions without sounding like an idiot.
DWZM's board has three 4101's on one board, and they are all controlled by one PWM signal. So if I wanted to break it out so that every 12 LEDs was on a separate PWM channel my two options would be too buy DWZM's board but only populate two of the circuits or design a new board that only had two drivers per board, correct?
Yep, or use a different board design. It would be super easy to modify my design to have separate PWM pins for each driver, or to hack one of the drivers off the board, etc.
FWIW since most (cheap) board houses have a pretty low minimum order, you might end up with way more boards than you need anyways, so only using 2/3rds of the circuits on each board might not be the end of the world. Plus it would be more copper per IC for cooling, etc.
My last question relates to dimming but is not driver related. Where do most people go to buy their Arduino boards? What Arduino accessories will I need to get the dimming and programming working for a LED driver. Lastly, how many PWM channels are their on a stock Arduino?
The Arduino website lists all approved vendors:
http://arduino.cc/en/Main/Buy
If you're buying an official board, you should buy from one of them. In the US, Sparkfun is probably the most popular. I also like Seeedstudio and Modern Device.
For a super-basic dimming arrangement, you just need an Arduino, an RTC module (DS1307-based is the most common), and some wire running to the drivers. That's it. If you want a display and input, then you need to get an LCD and buttons or some other input method. I'm not really a fan of putting complicated UIs on little controllers so my approach would be to not bother with a display unless you really want one - you can always add it later, for instance.
There was a "post your Arduino LED sketches" thread a week or two ago that had some code that would get you started.
gringabot, go ahead and post your EAGLE files and I'm sure you'll get some good feedback!