James –
I believe you are confusing an audience pixel, which is global to your entire site, and a conversion pixel, which goes on only a small number of pages. Kellen’s reply about pixel types (Checkouts, Registrations, Leads, Key Page Views, Adds to Cart, Other Website Conversions) are still all conversion pixels.
The custom audience pixel goes into the “Tracking Code” if your theme supports it, or likely inside header.php if it does not.