Is there a way to margin an anchor in css?

If the header is truly fixed then place your anchors in a scrollable div. Then the div containing the anchor will scroll instead of the entire page. Visit the fiddle and click on anchor1. It goes to anchor2. And so forth.

http://jsfiddle.net/mrtsherman/CsJ3Y/3/

css - set overflow hidden on body to prevent default scrolling. Use position absolute on the new content area with top and bottom set. This forces it to stretch to fit the remaining viewport window.

body { overflow: hidden; }
#header { position: fixed; top: 0; left: 0; width: 100%; height: 50px; background: gray; border: 1px solid black; }
#content { 
    overflow: scroll; 
    position: absolute;
    top: 50px;
    bottom: 0px;
    width: 100%;
    border: 1px solid blue; 
}

html

<div id="header">header</div>
<div id="content">
    <div>
        Page Content <br />
        <a id="a1" href="#anchor2" name="anchor1">Anchor 1</a>                
        <a id="a2" href="#anchor1" name="anchor2">Anchor 2</a>   
    </div>
</div>​

Welcome to the future:

.box {
  scroll-margin-top: 50px;
}

Source: https://css-tricks.com/almanac/properties/s/scroll-margin/