For primary color, all of these CSS values change:
::selection { background-color: #3b8dbd; }
::-moz-selection { background-color: #3b8dbd; }
a,
.themeform label .required,
#flexslider-featured .flex-direction-nav .flex-next:hover,
#flexslider-featured .flex-direction-nav .flex-prev:hover,
.post-hover:hover .post-title a,
.post-title a:hover,
.s1 .post-nav li a:hover i,
.content .post-nav li a:hover i,
.post-related a:hover,
.s1 .widget_rss ul li a,
#footer .widget_rss ul li a,
.s1 .widget_calendar a,
#footer .widget_calendar a,
.s1 .alx-tab .tab-item-category a,
.s1 .alx-posts .post-item-category a,
.s1 .alx-tab li:hover .tab-item-title a,
.s1 .alx-tab li:hover .tab-item-comment a,
.s1 .alx-posts li:hover .post-item-title a,
#footer .alx-tab .tab-item-category a,
#footer .alx-posts .post-item-category a,
#footer .alx-tab li:hover .tab-item-title a,
#footer .alx-tab li:hover .tab-item-comment a,
#footer .alx-posts li:hover .post-item-title a,
.comment-tabs li.active a,
.comment-awaiting-moderation,
.child-menu a:hover,
.child-menu .current_page_item > a,
.wp-pagenavi a { color: #3b8dbd; }
.themeform input[type="submit"],
.themeform button[type="submit"],
.s1 .sidebar-top,
.s1 .sidebar-toggle,
#flexslider-featured .flex-control-nav li a.flex-active,
.post-tags a:hover,
.s1 .widget_calendar caption,
#footer .widget_calendar caption,
.author-bio .bio-avatar:after,
.commentlist li.bypostauthor > .comment-body:after { background-color: #3b8dbd; }
.post-format .format-container { border-color: #3b8dbd; }
.s1 .alx-tabs-nav li.active a,
#footer .alx-tabs-nav li.active a,
.comment-tabs li.active a,
.wp-pagenavi a:hover,
.wp-pagenavi a:active,
.wp-pagenavi span.current { border-bottom-color: #3b8dbd!important; }
For secondary color:
.s2 .post-nav li a:hover i,
.s2 .widget_rss ul li a,
.s2 .widget_calendar a,
.s2 .alx-tab .tab-item-category a,
.s2 .alx-posts .post-item-category a,
.s2 .alx-tab li:hover .tab-item-title a,
.s2 .alx-tab li:hover .tab-item-comment a,
.s2 .alx-posts li:hover .post-item-title a { color: #82b965; }
.s2 .sidebar-top,
.s2 .sidebar-toggle,
.post-comments,
.jp-play-bar,
.jp-volume-bar-value,
.s2 .widget_calendar caption { background-color: #82b965; }
.s2 .alx-tabs-nav li.active a { border-bottom-color: #82b965; }
.post-comments span:before { border-right-color: #82b965; }
You can find CSS for all styling options in /functions/dynamic-styles.php