If you want the #header to be the same width as your container, with 10px of padding, you can leave out its width declaration. That will cause it to implicitly take up its entire parent's width (since a div is by default a block level element).
Then, since you haven't defined a width on it, the 10px of padding will be properly applied inside the element, rather than adding to its width:
#container {
position: relative;
width: 80%;
}
#header {
position: relative;
height: 50px;
padding: 10px;
}
You can see it in action here.
The key when using percentage widths and pixel padding/margins is not to define them on the same element (if you want to accurately control the size). Apply the percentage width to the parent and then the pixel padding/margin to a display: block child with no width set.
Update
Another option for dealing with this is to use the box-sizing CSS rule:
#container {
-webkit-box-sizing: border-box; /* Safari/Chrome, other WebKit */
-moz-box-sizing: border-box; /* Firefox, other Gecko */
box-sizing: border-box; /* Opera/IE 8+ */
/* Since this element now uses border-box sizing, the 10px of horizontal
padding will be drawn inside the 80% width */
width: 80%;
padding: 0 10px;
}
Here's a post talking about how box-sizing works.