I just checked using 'top' and I'm running @ 50% on one core. seems to be the core with the 5850 on it. What is eating it? o.o
Yeah you can use top, or pidstat or mpstat or iostat (not sure if you won't need sysstat installed, if so: apt-get install sysstat)
htop is convenient also to see cpu usage on each core (apt-get install htop)
50% is not normal btw, I get ~5-10% with same number of GPUs (2x 5870, 1x 5830) on an underclocked and undervolted E4300.
Is your BAMT up to date, did you do any modications to it? Have you got any other motherboards to try it? What is the CPU? Did you try to put the cards in different slots?