I don’t think you can add 2 background images to the same div/header so that’s why one goes away when you add the other. The image with the higher priority will always override the other image. You could try experimenting with border-image to see if that will work for you – http://www.w3schools.com/cssreF/css3_pr_border-image.asp
In order to align your logo with the nav you would need to either adjust the size of the logo itself, or increase the height of the Header….or adjust the padding in the nav on the right (line 1289) –
.genesis-nav-menu a {
color: #fff;
display: block;
font-size: 13px;
font-weight: 300;
letter-spacing: 2px;
padding: 30px 15px;
text-transform: uppercase;
}