I have the password gate installed but the pages I want to protect are public How do I make them privbate so I can add them to the gate?

Read the sticky at the top of the page.

I did read it and I did waht it said but the links are still showing and available ont the top bar.

Apparently you missed the very first sentence:

"The Password Gate is NOT server-side protection. it does not intercept users or prevent them from going to any webpage on your site. Only server-side security provided by your webhost can do that."

Links will always show unless you remove them from your page. the password gate doesnt change any pages, it is a gateway that visitors go through to whatever you want to show them on the other side of the gate.