I always shoot with the full 39 point AF when shooting sports, but otherwise I generally use a mix of full AF, partial AF or just the one point. Unless I don't have the time to recompose and need to quickly get the shot, one point generally does the job. If it's that important though, sometimes I'll pre-focus so that when the subject enters the frame the focus will already be spot on.
Regarding ISO, I never use auto ISO just so that I can have complete control over my exposure. I shoot using aperture priority mode 99% of the time, so if I need to adjust my exposure I'd rather change the aperture than the ISO. For example, in low light I'd rather shoot at f/2 and ISO 400 rather than f/2.8 and ISO 800. After ISO 800 on my D7000, I do see a fair increase in noise, so I don't like turning it too high. If that doesn't work well enough, I can always use my SB-700 flash and set my ISO again. Another example would be outdoors, I'd rather shoot at f/5.6 and ISO 200 than f/4 and ISO 100, the tiny extra bit of noise won't affect the IQ enough to justify setting the ISO down to 100, but the extra sharpness using f/5.6 over f/4 is quite a bit. Using Auto ISO doesn't give me the control that I like to have, which is why I prefer manual.
Gear: 7 Nikon Nikkor AI-S and AF-S lenses, SB-700 flash, Nikon D7000, Nikon FM, variety of accessories
"There are no rules for good photographs, there are only good photographs."
- Ansel Adams