Depending on whether you're tracking site-wide conversions or page specific conversions, you'll need to follow one of the following instructions.

Page Level

If the purpose of the pixel is to track conversion on a specific page, then it should be place at the top of the page template of that page – not in the theme files. The page template is found under Page > Template.

Site Level

If the purpose of the pixel is to track site-wide conversion, then it should be placed in the layout.html file of a custom theme. This is found under Theme > Current custom theme> Templates > layout.html. Full disclosure, you'll need to have a custom theme enabled to apply changes on the layout.html file.

From here, you'll want to navigate to the layout.html file. Most tracking pixels should be applied within the <head> tag of your layout. The <head> tag should be visible within the file (see example below).

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