Blog URL incorrect in confirmation email

I just installed the 'Subscribe By Email' plugin, and used the widget to signup as a first test.

It sent the Confirmation email, but the Blog URL listed is to the folder where I have WP installed, which is one level down from the actual URL of the site.

WordPress Address:
Site Address:

What is the best (and most maintainable) way of updating this?

If I do any CSS customization of the Widget input buttons, etc., what is the best way to do this?