Ok everyone, I appreciate your comments.
However, it's not a matter of it causing any problems. I know owners who don't even use the belly pans on their cars.
I post these "How to's" because I'm making my car as close to the way it was when new as I can. I try to do everything the proper way. If you don't want the clips to go through and hold up your belly pans, by all means, it's your car and you do what you want with it. This is my car and I am going to put it together properly or as close as I can get to it.