You have the code installed incorrectly if it is showing on some pages but not others. If you installed it per the instructions it will appear on all pages of the site including the checkout page.
You can track cpc traffic by then linking your Adwords account to your Google Analytics account and indicating to Google that you want to "Apply Cost Data" to your reports.
This will get you all the detail you need on cpc.
But again, you need to have the GA code installed correctly first and it appears that isn't the case.
There are only a few steps to installing this mod are you sure you are using this one (there is another mod that is not mine out there.)
If you can't figure it out, post a link and I'll see if I can't pin point what might be going on.
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