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You usually include the Google Analytics code in the header of your page template so that it loads on every page. Google recommends to paste both of these pieces of code right after the opening <head> tag in your document.
As to what is the difference between the two:
The first (Google Analytics Content Experiment code) is something you need when you ...
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Obfuscated javascript is still machine readable. So from the browser's perspective it's just code.
But it depends on your obfuscation, and it depends on the amount of code. Some obfuscation results in considerably larger filesizes -- which can increase overall pageload. It also results in slightly slower js code execution.
Both of those issues could in ...
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