I don't no whether this question is well-formed or not

Your first question sounds more natural.  But perhaps the question could be rephrased.  I am not sure that influential is the best word to use.  I suppose it could be true that classroom peer feedback, or teacher feedback has an influence on a student (influence: "the capacity or power of persons or things to be a compelling force on or produce effects on the actions, behavior, opinions, etc., of others"), but it seems like an awkward way to say it.

How about Which class provides the most useful feedback?  or In which class is the most useful feedback given?

"I don't know whether this question is well formed or not"

A: 1

In which class is feedback more influential?

The simple answer to your question: option one. Why? Generally you should never end a sentence with a preposition ('in'). You can choose to end like this, technically it is still correct; however, it makes for a weak ending, and a 'weak ending' makes for a weak question. 

If you don't want to spend much time on it, go for question one. However I think there is still room for improvement. Here is my suggestion:

Feedback is most influential in which class? 

A:2

Your original question was written in the passive voice. It seems to me 'feedback' is doing the influencing of the 'class.' This makes 'feedback' the true subject, 'class' the object, and 'is' our verb. If you can (you know the context better) make 'influential' a verb--here it functions as an adjective. I try not to use 'is' as a main clausal verb, it feels too plain. Though sometimes it feels like the only option. 

- is > weak verb (state of being: form of the auxiliary verb, 'to be')
- influence > strong verb 

- more or most? More gives the impression of numbers, where most gives an impression of impact.

So are we to have influential feedback, or feedback that has infulence on the class? Sometimes adding a character can help clarifying these questions. Who's feedback is it? Student, teacher etc...  

A completely different approach:

Student feedback *notably influenced which class this year?

* add any adverb you like: highly, greatly etc.. Hope this helps! - Iain