Implement header/footer from [url removed, login to view] into WHMCS, so that WHMCS looks/feels as mutch alike the main site as possible. This includes fixing buttons/css that conflicts or doesn't look good.
Important note: I would prefer to do as little changes as possible to the WHMCS-install/WHMCS files and templates if possible (so that it is easy to upgrade and not overwrite your custom changes). It is not always possible, but try!
So if there are things that can be done in seperate css file instead of modifying the WHMCS-templates, it is a big-big plus.