I tend to use auto ISO and manual mode together (zone shooter here, manual is loads easier for me than keeping an AE-lock button mashed).

Auto ISO is pretty handy, but keep an eye on the ISO in use when there's not much scene illumination, but there are still highlights that you want detail in, even though that ISO is below the limit you set.

With most digicams, ISO is, essentially, a gamma wheel. Noise comes from not-enough-photons, not from too-high-ISO. Letting the camera use a too-high-for-highlights ISO will blow those out. The only advantage is that it’ll be easier to see your shadow and black areas on the back of the camera. Once you’re in post, it doesn’t matter — so long as you’re shooting raw.

Finally: Do NOT use auto ISO for flash photography. It just makes things harder for no real advantage.