Gotcha. The SCLogin module has a popup mode for the login area. Simply set the "Login View Settings" option to "Modal Popup". Then, the login button will display the popup. There are other options to make the login button as text instead of a button as well.
For our site, the top right menu area is actually the SCLogin module. We just applied a few additional styles to have it look like our template. Our template has a module position in the top right to allow the SCLogin module to display there.
We hope that helps explain,
Alex