QUESTION Access/manipluate functions and classes to/from 3rd party plugins. Best practice?

[roy_b8te]

I need to add functionality and or call functions, class methods,
to and from 3rd party plugins for my custom theme.

I know I could add `cross directory` includes to a functions.php file in my theme's home directory,
but was wondering if this is best practice.

I also obviously do not want to edit the plugin's source as it could potentially break other themes usage of the plugin and still doesn't address the need for `cross directory` includes.

Thanks in advance for any advice or direction.