The ==mark== syntax and search facility both highlight the text by an orange background. However, you can affect their look in your userstyle.css:
mark { background-color: #BBDD66; } /* green for your own marking */
mark[data-markjs] { background-color: #F3B717; } /* orange */
mark[data-markjs].mark-selected { background-color: #CF3F00; } /* reddish orange */
Or, if you want green and orange switched, just:
mark[data-markjs] { background-color: #BBDD66; } /* green */
mark[data-markjs].mark-selected { background-color: #6B8E23; } /* dark green */
Your own markings do not add attributes to the <mark> tag, as the search mechanism does. More technical backgrounds can be found here.