How do I overlap elements containing shapes

What I want is for the two squares at each side to come together and become one i.e. one overlapping the other in the center of the wrapper. The problem I am having is that once they come together, one of the square drops down a level. Im not sure if this is achieved using jQuery or using CSS.

Please see my program here

$(document).ready(() => {
  $(".square").animate({
    backgroundColor: "red",
  }, 3000);

  $("#squareOne").animate({
    marginLeft: "+=45%",
  }, 800);

  $("#squareTwo").animate({
    marginRight: "+=45%",
  }, 800);
});

#wrapper {
  width: ...;
  margin: 100px auto;
  border: 1px solid black;
}

.square {
  width: 100px;
  height: 100px;
  border: 1px solid black;
  display: inline-flex;
  justify-content: center;
  align-items: center;
  margin: 10% 30px;
}

#squareTwo {
  position: relative;
  float: right;
}

#squareOne {
  position: relative;
  background: #fff;
}


}

<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
<body>
  <div id="wrapper">
    <div class="square" id="squareOne"></div>
    <div class="square" id="squareTwo"></div>
  </div>
</body>

Solution

If you want the squares to overlap, they have to be absolutely positionned.

Then, there is a calculation about the distance to be travelled...

$(document).ready(() => {
  $(".square").animate({backgroundColor: "red"},3000);
  
  // Calculate the slide distance
  // That is half the wrapper width minus the half of the square width
  let distanceToTravel = $("#wrapper").width() / 2 - $(".square").outerWidth() / 2;

  $("#squareOne").animate({marginLeft: distanceToTravel},800);
  $("#squareTwo").animate({marginRight: distanceToTravel},800);
});

#wrapper {
  margin: 100px auto;
  border: 1px solid black;
  position: relative;
  display: flex;
  justify-content: space-between;
  
}
.square {
  width: 100px;
  height: 100px;
  border: 1px solid black;
  margin: 10% 30px;
  position: absolute;
}

#squareTwo {
  right: 0;
}

<head>
  <meta charset="utf-8">
  <title>JavaScript</title>
  <link rel="stylesheet" href="styles/styles.css">
  <link rel="stylesheet" href="//code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css">
  <script src="https://code.jquery.com/jquery-1.12.4.js"></script>
  <script src="https://code.jquery.com/ui/1.12.1/jquery-ui.js"></script>
  <script src="scripts/fma_t5.js"></script>
  <meta name="viewport" content="width=device-width, initial-scale=1.0">
</head>

<body>
  <div id="wrapper">
    <div class="square" id="squareOne"></div>
    <div class="square" id="squareTwo"></div>
  </div>
</body>