I thought there was an easier way, but I guess not. The only way I can find now is:
1. Create a dummy layer on each map where you want a designer background layer. Make sure it has similar parameters to the background layer on a new map (you can't leave Tileset empty though, I guess).
2. Open the project's SGDK2 file in notepad.
3. Find the layer's definition in this file on a row like <Layer Name="Designer Background" Width="1" Height="1" Tileset="My Tileset" BytesPerTile="1" OffsetX="0" OffsetY="0" ScrollRateX="0" ScrollRateY="0" Priority="0" VirtualWidth="4000" VirtualHeight="4000">
4. Delete 'Tileset="MyTileset"' from the row and save.
Now this will be the background layer. (Basically any layer that is not associated with a tileset will be the background layer)
Do you have old maps that don't have a background? Why? Have you not added a background yet, or are they overlay maps?