In order to change the color for the bottom borders (the lines under the headings) in MediaWiki, you should edit the skin's main.css file.

For example, if you are using the default Monobook skin, the file you should edit is:

/home/user/public_html/skins/monobook/main.css

Look for the following code:

h1, h2, h3, h4, h5, h6 {
    color: black;
    background: none;
    font-weight: normal;
    margin: 0;
    padding-top: .5em;
    padding-bottom: .17em;
    border-bottom: 1px solid #aaa;

You should edit the border-bottom: 1px solid #aaa; line. For example, if you wish to change the border color to blue, the line should be changed to:

 border-bottom: 1px solid  #0066FF;