You need to set the limit screws before you end up with big problems like the chain coming over the top and going into the wheel. Treat Eagle exactly the same as any other in terms of set up, it’s just very sensitive to set up if you want it to work smoothly. The Sram website has a very good instructional pdf to follow.
My Eagle chain is very worn (I left it too long and a new chain won’t work with the old cassette now) but still shifts perfectly so I doubt its that causing the bad shifts.