The limiter and level settings won't prevent clipping-they act after the ADC.
For moderately loud stuff or louder, set your gain to low and keep your record levels at 100. I you need to set levels below 100 to keep the meters from going over 0 dB it won't prevent clipping, so it's best to keep them at 100 so at least you'll know if you're clipping. If the meters do go over 0 dB (and I think it has to be very loud to do that at these settings), all you can do to prevent clipping is to move away from the source until they are peaking below 0 dB.
For quiet stuff, you can experiment with the medium and high gains, but again keep the record level at 100, so you'll know when you're clipping (and of course if you go over 0 dB with the gain at M or H, your first response should be to set it to a lower gain setting).
You can set the level above 100, if you need to, to get more gain, but I'm inclined to think that you'd get cleaner gain by boosting with your editing software (especially if you record in 24 bits).