It appears I am having a conflict with the WPMU Dashboard and the one Wordpress offers. How do I res

I discovered the theme I was using for my website had a theme that appears to have come from the Wordpress theme choice and not the theme choices offered by WPMU. It appears to be very confusing in telling the difference between the menu choices. Are they under the WPMU Dashboard or are they coming from Wordpress Dashboard? I see two different color highlights on the menu, but the majority of the menu choices/selections have the same shaded/color highlight from the Wordpress menu.

How can I resolve this issue?

Thank you.