i am not sure i get what you are trying to achieve. are you on Aperture Priority mode? there are 3 settings for Auto ISO; min ISO, max ISO and min shutter-speed.
let's say the min ISO = 200; max ISO = 1600 and min shutter speed = 1/50.
if you are shooting indoor and the ISO shows 1600, it means that, at your chosen aperture, the calculated shutter speed is slower than 1/50 hence the ISO was raised all the way to 1600.
if you want the ISO to be lower (ie less than 1600), the first thing you should do is increase the aperture to the max. hopefully, this will increase the camera shutter speed to faster than 1/50 and your ISO will remain at 200.
if your aperture is ALREADY at the max, the only other thing you can do is to reduce the minimum shutter speed setting but here you run the risk of photo blur
the auto-ISO feature is one of the nicest features of Nikon cameras which Canon does not have. it's very useful if you learn to use it properly. i can't think of any reason to turn it off. however, sometimes, you may need to adjust one of the 3 settings depending on the situation.
the only restriction of Auto-ISO (on the D90/D300 but NOT the D700/D3) is that the min shutter speed cannot be faster than 1/250 (if i remeber correctly). there is a work-around this by using Shutter Priority instead.
hope the above helps.