Hi there,
the Site Library was created for new sites – although they can be imported on an existing site its not easy.
First i would recommend you create a backup of your site.
Second ask your Host if they can create a Staging site – this will provide you with a copy of your existing site that you can make changes to without effecting the live site.
From the staging site you would:
1. Import the new site
2. Repair the changes you don’t want – they are:
a. Replace the logo the site imported.
b. Replace the menus the site imported.
c. Remove the posts, pages and media that was imported.
3. Check the site for any breakages. Fix them as necessary.
If all correct – ask your Host to Push the Staging site to the Live Site.