I'm sure cudaminer autotune is good but can you manually tune cudaminer?
Dang bro, how did you find about autotune but not the manual selection mentioned directly thereafter?
Well anyway, cudaminer will list tested "tuning" with the debug option (-D) but you should run on each card individually with -d. You can then use your "tune" choice with the --launch-config option.
cudaMiner has a readme, I have never used cudaMiner but I can read. Best of luck!