Setting up a campaign in Pardot for tracking behavior on a website seems to be an easy thing based on instructions that Salesforce provides, but my question is more about best practices for how many campaigns should be used for a single website. Is it best to use a single campaign for the entire website or set up multiple campaigns for different areas of the site?
According to this document:
Pardot campaigns are typically thematic touchpoints (similar to “source” in other systems) and are used to track the first touch you have with a prospect.
I know it's kind of confusing at first glance, but the thing to remember is that a campaign has a theme. For example, you might have a sale on Cinco de Mayo, and you want to have some Google AdWords, a drip mail initiative, flyers, and billboards, but all centered around this one day sale. You might get more granular and split each medium into different parts, but generally speaking, you want to know how successful a particular initiative is, so you'll link them all together as a campaign (think "marketing campaign").
So, in general, if you have one website per marketing initiative, then that's fine, go ahead and have as websites as you need. However, most companies only run one, or a few sites, and instead have landing pages. In this case, one website may contain dozens or hundreds of landing pages, each linked to a specific campaign, depending on your marketing initiatives.
If I were in marketing, I would probably prefer to have each separate ad group or promotion be its own campaign to compare the effectiveness of it to other campaigns so it be tweaked or new campaigns introduced that are iterative improvements over those that were successful.