Hey,
From looking at your screenshot I am a little bit confused. What are you trying to build here? Is this a "shield" for the arduino?
Usually when designing a shield for the UNO, you just provide some male header components (https://a.pololu-files.com/picture/0J1036.1200.jpg?910aac980aeb046ae0f78e75892f7404) that will connect to the pins of the arduino and you do not actually include the arduino in the design. You then route to this "header" in the same way as you were planning on routing to the arduino now. The problem with what you are doing now will be that if you generate manufacturing files or send them to someone that does this for you (e.g. send to OSHPark, generate gerbers, ...) all the data of the arduino will be duplicated in your board and it will not be created correctly. You only want to build your own PCB, as you already have the arduino. This should be reflected in your PCB design.
The orange lines (layer 20: dimension) indicate the physical "board outline" in EAGLE (the edges of the PCB). This means that you are trying to put signals (copper tracks) over a physical barrier, which is impossible. As you have "obstacle avoidance" turned on, the system will not let you do this (which is good 😉 ). As you can see on picture 2, once you moved the arduino inside of your board area, it got interpreted as a hole by EAGLE. You can see this by the color difference (background grey v.s. black board area). This is our way of indicating that something is going wrong.
Look at this example of a properly designed EAGLE shield: https://www.sparkfun.com/products/12660. Under Document you can find the eagle .sch and .brd files. Second to that, there is also a post available on the Autodesk blog about arduino shields, which might contain some interesting notes: https://www.autodesk.com/products/eagle/blog/arduino-shield-buying-designing/.
Pieter-Jan Van de Maele
Senior Engineering Manager, Fusion Electronics