They are kinda in the middle.
They are hardcoded to obey Eggman no matter what after a while of their shenanigans.
But also try to find loopholes when the doctor doesn't give direct orders.
Like when they got told to come back to base, Eggman didn't say at which time so it isn't in violation of orders.
But they also care for the doctor as seen on the IDW issue for the doctor birthday.
They are probably in hinding seeing as the D6 are a very heavy threat to them, as showing up too early could mean they get controlled.