There is no difference (the mod makes it easier without the need to "touch code" from within the Admin).
By the way, I would recommend that if you are going to insert the code yourself, then don't insert it into the header file. I would recommend inserting it into the "tpl_main_page.php" found in the "common" folder (includes/templates/[your template]/common ).
That is the better place to put it (and the spot that the Simple Google Analytics inserts it).
I have inserted the Google Analytics code (along with e-com tracking and conversion tracking) on older carts just by pasting into the bottom as indicated here. Again, the mod provided makes it a bit easier. (Why not take the "easy route")?



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