Is the position of 都 in a sentence important？ (example inside)
In my opinion, 你週末通常都做什麼 is more natural.

你週末都通常做什麼 sounds ok, but not as natural as the first one. 

There's no difference in meaning. I don't think there's a strong reason as to why the first one sounds more natural. It might be all about conventions.

Note that some might take this differently based on their conventions. 

By the way, 都 here is used to emphasize, not to convey every or each.