Create the mxml component for your side boxes. In the following, I based it on VBox since that might be what you're looking for. I gave it an obnoxious backgroundColor that should be easy to spot when we run the app.
SideBox.mxml
<?xml version="1.0" encoding="utf-8"?>
<mx:VBox xmlns:mx="http://www.adobe.com/2006/mxml" width="100" height="300"
backgroundColor="0x990000">
</mx:VBox>
So in your main mxml application you can include your custom component by telling the application what namespace to look for it (that's what the xmlns:local="*" is for - the word local is just a name so that I can easily remember what it means, you can call it anything, the * essentially means to look in the current/same directory).
Main.mxml
<?xml version="1.0" encoding="utf-8"?>
<mx:Application xmlns:mx="http://www.adobe.com/2006/mxml"
xmlns:local="*" layout="absolute">
<local:SideBox x="40" y="20" />
<local:SideBox x="500" y="20" />
</mx:Application>