Lefteris,
You need to place your div in the mani-page div.
<div id="main-page">
<div style="height:50px; width:100%; text-align:left; background-color:#3892D2"/>
<div id="jimu-layout-manager"></div>
</div>
and set the main config.json map objects top property to 50.
"map": {
"3D": false,
"2D": true,
"position": {
"left": 0,
"top": 50,