первый способ делает это в таблице. Вам просто нужно использовать 3 ряда и переставить свои клетки. Второй способ, вероятно, предпочтительнее и использует flexbox
<div id="mapControls" class="container">
<table>
<tr>
<td><input type="checkbox" id="births" checked="checked" onclick="toggleMarkerGroup('births')">Births</td>
<td><input type="checkbox" id="burials" checked="checked" onclick="toggleMarkerGroup('burials')">Burials</td>
</tr>
<tr>
<td><input type="checkbox" id="marriages" checked="checked" onclick="toggleMarkerGroup('marriages')">Marriages</td>
<td><input type="checkbox" id="migration" checked="checked" onclick="toggleMigration(migrations)"> Migrations</td>
</tr>
<tr>
<td><input type="checkbox" id="deaths" checked="checked" onclick="toggleMarkerGroup('deaths')">Deaths</td>
<td> </td>
</tr>
</table>
</div>
#container {
display: flex;
justify-content: space-evenly;
}
#left,
#right {
display: flex;
flex-direction: column;
}
<div id='container'>
<div id='left'>
<span> <input type="checkbox" id="births" checked="checked" onclick="toggleMarkerGroup('births')">Births</span>
<span> <input type="checkbox" id="marriages" checked="checked" onclick="toggleMarkerGroup('marriages')">Marriages</span>
<span> <input type="checkbox" id="deaths" checked="checked" onclick="toggleMarkerGroup('deaths')">Deaths</span>
</div>
<div id='right'>
<span> <input type="checkbox" id="burials" checked="checked" onclick="toggleMarkerGroup('burials')">Burials</span>
<span> <input type="checkbox" id="migration" checked="checked" onclick="toggleMigration(migrations)"> Migrations</span>
</div>
</div>