How do I merge two .stl files in Cura 2.7 (for 3 Extended) to do two-color print?

[PatrickW 0]

Each of these disks are 50mm in diameter. The blue one is 8mm tall and the yellow is 1mm tall. I want to merge the two files so that the blue is sitting directly on top of the yellow and each is printed a different color using a different extruder. I've selected all models and merged them but every time something different goes wrong. The first time the merge appeared to be successful but then the two models didn't adhere to each other after printing as if there was space in between the two. The second time I tried merging them the yellow one kept being placed on top of the blue one with space in between the two. The third time the yellow one was merged inside of the blue one. Thank you for your help.