I am not sure how you are adding a PiCap to a model? You don't need to delete any models. If you assign the correct start Universe and start channel to your models and the controller port connection and then set up the controllers to match your XLights setup then things should work. You can also use XLights to set up your controllers for you if you want and to simplify life. I think once you understand things it will start to make sense.
Let me see if I can clear things up.
Think of your show as a big city that needs mail. Each pixel needs a unique address so that the controllers (postal Delivery men) can deliver the information to the correct pixel (color, brightness, etc.) you can use absolute addressing and forget about Universes and channels and just start at 1 and keep counting up for the number of channels you need (3 channels for each pixel) but this can get confusing for some people, especially when you start moving models around or changing controllers because you will need to keep track of what "house" comes next in the delivery process, which might span several streets, ..which street first, then which street next, etc. So we can break things down into Universes and Channels to simplify how you are going to identify each pixel's location. So now we can break your city down into smaller sections, kinda like streets. So now you just need to know what street (universe) each "house" is on and what house you are going to start delivering on. You are the Postmaster for your city, so you get to decide how you want to assign "streets" and what works best for you. Keep in mind that you will then have to tell your mailmen (controllers) what houses they have to deliver to. After you design your city so that you can identify each pixel, then you need to tell your postmen "controllers" what houses they are responsible to deliver the information to. You can set up all of this information in XLights, and then use XLights to tell the postmen (upload to controllers) who they are responsible for delivering the information. I hope this makes sense and if you are having problems, include some screenshots in your next post and we will get you straightened out. XLights has a backup of your setups and depending on how you have your backups set up, you can always go back to a previous set up if you get things too screwed up.