I have kilts that have three straps, and I have a kilt that has two straps. I think I prefer the three strap variety, but I make sure the hip strap is at least one hole/inch looser than the waist, so that it doesn't affect the way the apron hangs. I also like to wear my kilts a little higher than some, so that the lower strap is above my hip rather than on it.

On my Canadian military Black Watch, which is very high waisted, the third strap is not an option... it's a necessity. As Matt said, the lower strap is at my waist, and the upper strap is up on the rise, closer to my ribs.