I am assuming you have created assembly panel and are ready to place score.
Also, that you are in fablink
1. Go to Draw mode
2. Select add line
3. Right click on screen select properties on popup.
4. Click on layer selection, select scoring line from pull down.
5. you can make scoring line solid or dotted. ( I use dotted)
6. You can now close properites window and draw line where score is desired
7. All this still needs to be documented in fabrication notes and dimensioned.
You might want to talk with your fabrication vendor about what they need to see as far as documentation.
One last thing. I am sure you already know but am mentioning anyway. Both boards need to use the same stackup if you want to put them on same panel.
Was this done using PADS software?
The layout was done using Mentor Expedition. The panel was done using Mentor Fablink. I believe what you are going to have to do here is draw panel manually or use a tool that can create a panel such as CamCad or Cam350. (camcad was recently bought by Mentor) Have you talked to your fabrication vendor in regards to nomenclature? They should be a good source of info.