1. First you need to create two maps in fusion table, and copy this script from GitHub.
2. Open script in any text editor and change lines
[74-75 and 94-95] This is your Fusion table ID and geocoded column. You can use FT Wizard to get this data if you are not sure.
3. Save new file and just remember that both maps size should be the same (width and height).
4. That's all now you should see your maps with swipe effect.
TIP: You can also disable some of the Map function for better performance. Just paste option after line zoom:2 [69 and 90].