When you're entering your animal onto the Moocall Breedmanager system, you can enter their breed.

If you can't find your cow's breed from the list available on the app, you can select custom breed and type in the name yourself.

If it is a cross-breed, select one breed in this menu. When you do this, a screen pops up, giving you the option between Finish and Crossbreed. Select crossbreed.
From here, you can select the second breed.