Okay, I go into my file manager and I edit the html.. I put stuff such as a counter in there and when I publish my web, then all the stuff I added is gone? What the hell is going on??
"Publish" is part of the Website Wizard. By using "publish" you are explicitly instructing the server to replace your File Manager changes with what you saved last in the Wizard.
You can use one editor or the other, you cannot mix them.