In order to keep the element from going out of boundaries on the right side, you should be setting the right property instead of the left.
.Logo_wrapper{
position:absolute;
top:40%;
right:5%;
z-index:10;
}
Updated fiddle: http://jsfiddle.net/NCZg8/6/
Also i would not like to put relative position to the element since it puts a large margin between header and Navigation Bar.
In order for the logo to appear inside the header, it's important to set position:relative
on the header element. To see a more detailed explanation of relative and absolute positioning, see here: http://css-tricks.com/absolute-positioning-inside-relative-positioning/
Your problem of margin can probably be fixed with css.