leave some processor time for your atmega to actually perform some calculations yeah?
Bit more power hungry this way
A long time ago I wrote some code that did 5bit software PWM with such a matrix. It took 50% of the cpu load.
Too much information leads to paralysis by analysis, but have you considered the PCA9626:The PCA9626 is an I2C-bus controlled 24-bit LED driver optimized for voltage switch dimming and blinking 100 mA Red/Green/Blue/Amber (RGBA) LEDs.
polhemic if you could get the board your talking about up to 350/400 mA for 1 watt rgb led's i would be interested.