"What did you do last night?" is a correct sentence in past tense 

"What were you do last night?" is a wrong sentence. Maybe you mean "What were you doing last night?". This is a past continuous tense.

Both can be used to ask about something that happened in the past, however, the context is different. "What were you doing last night?" is asked when you are referring to an ongoing past situation, such as "What were you doing last night when .... ?".

Simple. 1st one is grammatically correct while the 2nd one is not. 

2nd one might be:

1# what were you doing last night?

Or, what have you done last night?

@That would be what is the difference?

##(Your question)

Let me know if u have any other questions.