I'm not a native English speaker but I would say "so are we friends now?" because the auxiliary verb, that is "are", should be before the subject(we) and normally at the beginning of the phrase. The "so" sounds really strange and unusual being at the center of the phrase, because it sticks together two phrases. Also, "from" is unnecessary but I'm not that sure of it. Just because, I'd rather not use it. I repeat that I'm not a native English speaker so there may be something wrong

We are SO friends from now This is slang and is not correct. You might hear it in spoken English by school children but you would not see it written. The SO is pronounced loudly for emphasis. Correct examples would be : Are we friends now? We are friends. We became friends when we met on holiday.

If you are trying to ask if this person is your friend now, you would say "So are we friends from now on?" "I am so friend with you" - I'm not sure what your trying to say here but you can say: "I am good friends with you" to tell this person you have a close friendship with them. Or If you are asking them whether or not you are friends with each other you would say "So, am I friends with you?"