PPC is a channel for advertising, and as such, it can be used to accomplish many different goals. Your website should be set up to get optimal results based on the primary goal of your website. Or, to be more precise, your Landing Pages should be set up for maximizing the primary goal for visitors to that page.
Since a website might have many sections, that each has different goals, you should focus your PPC campaigns to generate traffic that matches the specific “primary” goal of each individual section, and each individual product or service.
Since there are potentially many different goals, each website landing page should be optimized for that specific goal, and proper keywords selected that are extremely relevant for that specific goal, and then ads written that are clear concise and compelling are created for each ad group that targets the most relevant landing page.
For example, let’s say that you are talking about an eCommerce website that sells a full range of clothing. You will want to create a navigation menu for the homepage and category pages to help users browse and find whatever they are looking for. You may want to create categories for age groups (children vs. adults) and/or for gender (men’s, women’s, boys’, girls’), then subcategories under each main category for clothing type (shirts, tops, pants, skirts, etc.) The concept here is to organize each item into categories of similar products, going from general categories down to highly specific categories.
Each category page will be a potential landing page, as well as each product page. Create at least one ad group for each category, and select the most specific landing page possible for each keyword and include that keyword within an ad group that targets that landing page.
The key concept here (segmentation) is to always select the most specific and relevant landing page for each keyword you are targeting, this often requires splitting your keywords into many different ad groups. And then write ads that clearly target the specific landing page and keywords contained within.
At the other extreme, you might have a website built with the goal of generating leads for your sales team. This type of website would naturally be organized very differently from an eCommerce website. Since the typical goal is to generate a lead by having the visitor fill out and submit a form, a much simpler website will usually perform better. You might even segment the website so that visitors see only one page of the website, with navigation links removed, and the only available action being that of filling in the web form.
If the goal is lead generation, then it typically is best to design many different landing pages, each tailored to match the precise value proposition and message of a particular set of ad groups. Again this allows you to segment your targeting and communicate a message that is crafted for that specific segmented target group.
Of course, there are many other potential goals, the point I am making is to tailor your website design, and campaign structure, to meet the precise needs of your users, using as much segmentation as needed.
I hope that helps you to understand the general approach. If you want more specific advice, then give us the specific goals of your campaign and we can suggest the best approach based on the specifics needs of your planned campaigns.