The second one:
Not only did he..., but he also did...
Not only did he do this, but he also did that.
That phrasing is preferred.
He not only went to hawaii, but he also went to cancun and aruba.
The other example is unusual and awkward since the subject of the sentence is "he" and it should be clarified as such. "Also" describes the word following it....and it should be "also did" something rather than "also he did" something. It should go right before the verb that it is describing as "also".
... and more
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