You could add padding to the .head-wrap
like this – padding: 20px 0 0;
…..and adjust it until you get the effect you want.
If you do that, then you’ll need to decrease the padding on the .header-image .site-header .widget-area
on line 1975
…then the padding on the menu links as well – .menu-item a
on line 4184
Before you upload your logo, you need to change the size in your functions.php file to the exact size of your logo, then you won’t need to crop. Here is a tutorial you can check out for that – http://www.carriedils.com/add-logo-genesis-theme/