1. The correct question is "How are your studies going?".
Note that 'studies' is a plural noun, so it needs a plural verb: 'are', not 'is'. You don't need the word 'on' - when you're asking about the progress or success of something, you only need the question word 'How' and the verb 'go'. For example, "How is your job going?"or "How did your exam go?"
2. The correct answer is "They're going well".
Because 'studies' is plural, you need to say 'They' (not 'It') and 'are going' (not 'is going).
You also need to use the adverb 'well' rather than the adjective 'good'. This is because this word is modifying the verb 'go'. It sounds very uneducated to say that something is 'going good'.