You can use your own EnlighterJS Themes by uploading them into a directory named enlighter/ within your theme (you have to create it by your own).
The full documentation about external themes is available here.

Please pay attention to the different theme types:

Type 1: Public/Payed WordPress Themes

• Themes like WordPress buildin `twentytwelve` or `twentyten`.
• Attention: It is strongly recommened to create a Child Theme to protect the created enlighter/ directory from being erased during the update-process!

Type 2: Custom/Selfmade WordPress Themes

• Custom themes are created by your own and you manage the update-process by yourself. There is no danger by adding additional directories to your theme!