You’re really not supposed to ask CSS questions on here but I’m procrastinating…Right now your yellow nav bar is .nav-menu. Yes, you added the padding but the padding is pushing the content inside the nav bar to the right. Padding pushes things inside elements around the inside vs. margins which are spaces outside an element. So you could change the max-width of the nav.menu to 400px or so and then it won’t be so long.
You have your green box in the #main.wrapper…which is a different place than where your nav.menu is (it’s in the header#masthead.site-header). Since they are separate areas they have separate spaces and boundaries.
I think you have more of a design issue than a CSS issue. (I’m more of a front-end person than a back-end person). If there is enough length for the whole green box then you would either have to create another box for something under the yellow nav bar or there would be a large white space, does that make sense?
My design advice is to create a widget area in your header so that you can display the menu in the green header image – not through photoshop or something like that, but in a new widgetized area so the menu will display over it. You can use white or yellow on the green and it will be very legible. Then divide your content into two columns, or a column and a sidebar, and the top of the green box will line up with the top of the content text.
Also, since I was poking around your site, you have a background color that shows up under the green box. It’s from here:
.widget-area
{
background-color: #fbe2a8;
}
Let me know if that helps at all.