I have a website www.rypintoit.com
Everything past the welcome page is restricted to members only.
I am having a problem as all my files are uploaded to the main root directory so setting the access gets confusing. Can I put all the restricted pages in a private folder so that all I have to do is grant members access to that folder giving them access to everything in one bulk?

I have therestricted areas hidden right now but if you need to see what i am talking about you can access it by going to

http://www.rypintoit.com/SiteMap.html (everything linked from this page is restricted except the calendar and members music)

What you would do here is make two websites. The first is your main website that is open and the second you publish to a sub-folder like "members". You then would use Access Manager to protect the members folder and everything under it.

That is exactly what I thought but would I need to change the links for all the stuff in the members folder? Or Just the one Login Link on the main page?

The unrestricted website would only be one page if I'm interpreting you right. There would be a link to the restricted website index page that could only be accessed if you have a username and password. The restricted website would be built just like normal. No special link modifications at all.