PHP includes

I'm working on learning php and have been toying with includes, and I am trying to figure the advantages/disadvantages to using them. I know that using them eliminates the need to "put" the files once altered as with a template, however, is that the only advantage. My particular concerns are with SEO and if the search engines and the bots can read the page if it is made completely on includes? Any and all comments would be appreciated. Gary