basutton,
It's dangerous to follow a post by the Boss...but here goes anyway.
No, it won't hurt the clay to sit. The compacted depth recommended by the USDA Bible is 12 inches. I posted the direct quote from them in another post, but don't have it handy...can do so tomorrow if you wish.
Having said that, my experience says go with a margin of safety...I use 24 inches, based on experience of never having it fail and having and old East Texas pond guy tell me to use 24 inches of packed clay for fixen leaks. Two feet of good clay will not leak and you will never have to worry about it again.