I don't understand much of this thread.
I would like to know how to protect the sites.

Every single one of my index and default files was
attacked since yesterday.

In your messages, I noticed mention of forms and
MySQL attacks. I don't know anything about
MySQL

But, I'm wondering if the attack coincided with my
installing PHP Lists from Simple Scripts. I installed
this yesterday, and re-configured the pages. Could
one of the forms be the opening for a badware attack?

If so, how can I protect the sites?

Thanks