I have a 6600 and I have FMQ'd with CT thread - I had it both top and in the bobbin and I don't have the blue dot bobbin case so I was just using the regular case; I think I did adjust my top tension though. (Sorry, I can't remember if I had to loosen or tighten; I think I loosened.)
My FMQ skills are pretty bad so my lines went all over the place, but I didn't have eyelashing or blobs. I've only ever gotten eyelashing on curves; now I set my stitch speed to about 2/3rds speed when doing FMQ and that fixed that.