Ok, so to get started, it seems you used the "background plugin" to set the blue background? If you are to re-style the website globally (all pages) with many elements, you might as well do everything from
Settings > Custom > Custom CSS instead, first disabling the plugin.
Settings > Custom > Custom CSS:
body, .sb-site-container {
background-color: #000099;
}
.pagenav-fixed .pagenav-link {
background-color: #000099;
}
.up-sidebar button {
background-color: #000099;
}
.sidebar-right a, .sidebar-right li {
background: none !important;
}
The last one will remove backgrounds entirely. It will be complicated to custom-color the menu, as it has shades of colors based on menu depth, menu open/closed, :hover, :active and variations for different screen sizes.
I'm guessing there will be more, because there are loads of elements with colors in variations of the selected skin. Just le me know! Personally, I would not use a strong background color like that for a website, as it's difficult to read and view in general. Under most circumstances, one would use company/branding colors for primary colors, on logos, buttons and headers, but on a simple light or dark background. It would be easier with X3 also.