You don't have to "include" plugins. Plugins operate, or should operate, by means of the extensive "hook" system built into WordPress core. Once activated, a plugin should not require much else (with a few exceptions for very complicated plugins).
What you need to do is make sure that you are using the appropriate Core functions classes to generate content-- such as get_header(), get_footer(), the_content(), the_title(), WP_Query, get_template_part(). It is a very, very long list.
This related answer might help: http://wordpress.stackexchange.com/a/103644/21376