If your header menu is overlapping with logo box, please go to the “Theme Options > General Settings”. In drop-down list “Menu Item offset” select which menu item should get the left indent to avoid overlapping with the logo. For example, if is your logo overlapping with the fourth menu item from left, select “4″. Then type into the field “Offset value (px)” numerical value of the offset – by how much pixels should the selected menu item be shifted from left. For example, type here the value “350″ and then see, how it looks. Then, if necessary, increase or decrease the value of offset.