By default, your end user will see a documentation screen that looks very similar to the following:
Notice that the ENTIRE screen is used and overrides your theme completely. This is intentional and cannot be changed unless you modify the plugin directly.
However, you can change the colors, fonts and logo to match your brand. You can also change menu options, some of the footer verbiage and the url that is triggered when the user clicks the logo area.
To make these changes simply navigate to the DOCUMENTATION->SETTINGS->CUSTOMIZATION tab. There, you will see the following items:
Make the changes you wish and then click the SAVE CHANGES button at the bottom of the screen.