When we encrypt-then-MAC, how do we defend the 2 parts? When we encrypt-then-MAC (which is the recommended case), do we send both in the same package? Both can be modified along the way, isn't it? how do we defend the 2 parts?
When we encrypt-then-MAC (which is the recommended case), do we send both in the same package? 


Yes


  Both can be modified along the way, isn't it?


Yes, but not without the MAC check failing.


  how do we defend the 2 parts?


You don't need to do anything else. The MAC is the protection.