In the Autotune -> Facebook App -> Page Tab area, you can set the Page Tab URL to whatever page on your site you want to show. That page will be shown whenever a user clicks into Page Tab from your Facebook Page.
For the Page Tab URL you specify in Autotune (for the Facebook Application you created and set in JFBConnect), you can also configure a special template and even a "Reveal Page" if you want to force users to click the Like button in your Facebook Page in order to see the actual content from your site.
To create additional pages, you simply need to create more Facebook Applications. In the Facebook developers area for that Application, you set the Page Tab URL, similar to how you do it through Autotune. You can add as many Applications to you FB Page as you want and JFBConnect won't have a problem with multiple pointing to your site. You just need one that JFBConnect is in control of for authentication, reveal page, custom template and other features.
I hope that helps explain, but if not, just let me know.
Thanks,
Alex