3rd party plugin with changes in native files into WP-theme - how to?

I’m going to use plugin from codecanyon in my new WordPress theme. I’ve already bought the licenses and I have written permission from the author. To customize the plugin to a theme I have to make several changes in native files and I wonder what is acceptable method to make that kind of changes:
1st way. Does the plugin has to be attached to the theme in its original version and only way to make changes in it is by creating an extensions to that plugin, inside my theme?
2dn way-prefered. Can I make changes in the plugin and attached it to the Theme in modified version with changed name, like thePlugin (itszy modified version)? It would be the most convenient option for me.

Thanks for help.

hello, anyone?