Thanks for writing to us.
Can you explain why the footer uses 2 bars?
The default footer using two bars because the first one is for widgets and the second one is for the copyright section.
You have to add some widgets from Appearance -> Widgets to show widgets in the footer. If you want to hide in just going to Theme Options -> Footer -> Footer Widget Areas -> Choose None from here.
Where is the second bar showing up?
The First bar showing up just before the copyright section. It will be shown by adding some widgets.
Also, how do I change the hover colour of the links?
To change color of nav bar links on hover just edit that Navigation Inline element , Then go to Top links -> Text -> Primary text color -> Interaction.
Change the colour from here.
Hope it helps you.