Do from is an ‘Indianism’, so use of this phrase must be referred to speakers of that dialect.
In Standard English† we use at with the verb do; the preposition phrase names the place where the work was performed:
I did my doctorate at the University of Wisconsin.
He did an internship at Microsoft.
We use from in this context with receive; the preposition phrase names the entity which conferred the gift:
I received my doctorate from the University of Wisconsin.
In ordinary speech, however, we use the verb get, which may take either preposition phrase (though at is probably more common)
I got my bachelors at Vanderbilt.
I got my bachelors from Vanderbilt.
With do we use at;
In a question, no preposition at all is needed, whichever verb you use:
Where did you do your bachelors?
Where did you get your bachelors?
Where did you receive your bachelors?
†By “Standard English” I mean English usage which will pass unnoticed with any educated native speaker—appropriate to its register and not dialectal, foreign, antiquated, or precious.
When asking any question indirectly, you must use sentence order and not question order.
So in the first example option 1 is correct, and in the second, option 2 is correct. This applies to both speaking and writing. (It is possible, however, in writing, perhaps in an interview write-up to do something like this: "He asked the President, "Where the hell are we?")
To make it easier to understand, think about an indirect question. That is, 2 questions combined into one.
Do you know?
Plus
Where is the bank?
When we combine the two, we will end up with one question (Do you know?) and the second will become "the details" which we can't phrase in question order.
Do you know where the bank is?
Question | Details
Best Answer
Number 1 is correct.
When we construct a statement -- not a question -- in English, we normally phrase it subject / verb / object. Like "You / go / to the store." When there's a "helping verb", like "will" or "do", it goes with the verb. "You / will go / to the store."
But when we construct a question in English, it's normally "interrogative word / helping verb / subject / regular verb / object". By "interrogative word" I mean a word like who, when, where, how, etc. So, "Where / will / you go?" "Why / did / Bob / leave?" Etc.