If you download the BlinmM datasheet http://thingm.com/fileadmin/thingm/downloads/BlinkM_datasheet.pdf on page 23 & 24 you will see sample code on how to control multiple BlinkMs. There is also an example in the Arduino examples they supply.
The BlinkM is I2C and each can be assigned a unique address. Each of the commands you send begins with an address, so controlling multiples should be pretty easy, albeit expensive in your case.
If you look at page 25 you will see that the BlinkM is really another microprocessor (Tiny45S) with an LED attached. It has a program loaded in it's itsy bitsy self. I'm not sure what the chip alone would cost, but by the time you bought the programmer, chips, boards, etc. for something like your planning it might not be the way to go.
However, a BlinkM solution should be pretty straightforward. It would also be cool as hell.
I'd suggest you buy one and mess around with it. It's an easy way to get familiar with I2C and the colors it produces are amazing. The first one is pretty cheap 