In my opinion, the easiest fix would be to introduce a new rule in your CSS file
.menus .main-subs.active { display: block;}
Then, update your function like this:
$('.menus >li').on('click',function() {
$("a", this).siblings('.main-subs').toggleClass("active");
$(this).siblings().children(".main-subs").removeClass("active");
});
$('.menus >li').on('click',function() {
$("a", this).siblings('.main-subs').toggleClass("active");
$(this).siblings().children(".main-subs").removeClass("active");
});
.menus { display: table; width: 70%; height: 76px; }
.menus li { position: relative; display: table-cell; height: 48px; padding: 0; text-transform: uppercase; font-size: 17px; font-family: 'Myriad Pro'; text-align: center; }
.menus li:hover {background:green;}
.menus li.order a { color: #ffffff; }
.menus li.order .main-subs { display: none; }
.menus li a { width: 100%; height: 48px; padding-top: 28px; display: block; color: #b1bbbe; }
.menus li a:hover { color: #fff; }
.menus li:hover { background: green; }
.menus li.current { background: #0383E7; }
.menus li.current a { color: #fff; }
.menus .main-subs { display: none; position: absolute; width: 100%; left: -40px; top: 76px; z-index: 999; }
.menus .main-subs.active { display: block;}
.menus .main-subs li { display: block; height: 51px; padding: 0; border-bottom: 1px solid #0383e7; text-align: left; text-transform: uppercase; background: #0870d3; font: normal 12px 'Malgun Gothic'; }
.menus .main-subs li a { display: block; height: 31px; padding-left: 12px; padding-top: 20px; color: #fff; }
.menus .main-subs li:hover { background: #0866c5; }
.menus .main-subs li:last-child { border-bottom: 0; }
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<ul class="menus">
<li>
<a href="#">Main Menu</a>
<ul class="main-subs">
<li><a href="#">Sub Menu 1</a></li>
<li><a href="#">Sub Menu 1</a></li>
</ul>
</li>
<li>
<a href="#">Main Menu2</a>
<ul class="main-subs">
<li class="withsub"><a href="#">Sub Menu 2</a>
</li>
<li class="withsub"><a href="#">Sub Menu 2</a>
</li>
<li><a href="#">Sub Menu 2</a></li>
</ul>
</li>
<li>
<a href="#">Main Menu3</a>
<ul class="main-subs">
<li><a href="#">Main Menu3</a></li>
<li><a href="#">Main Menu3</a></li>
<li><a href="#">Main Menu3</a></li>
</ul>
</li>
</ul>