You don't have to "include" plugins. Plugins operate, or ***should operate***, by means of the extensive ["hook" system][1] 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


  [1]: http://codex.wordpress.org/Plugin_API/Hooks