First, I would recommend against it.
I have a package of plugins that I use on almost all of our websites (both public and internal plugins)… and plugins should really remain plugins. Deploying a package of plugins is not hard or time consuming and only needs to be done once per project.
By integrating them into a theme, you lose the ability to activate/deactivate them if necessary, nor can you update them. Please consider that first.
Ok, so to incorporate them into your theme, this is what you would do…
- Create a “plugins” folder within your theme.
- Place both plugins in that folder.
- Within your functions.php file, use require_once to load each of the plugins default php files (if the plugin authors correctly followed convention, the main plugin file will be the one that matches the plugin folder name).
- Done.
Please also take note that you may have problems with activation/deactivation functions… so be careful.