Backup selecting files

Hello,

I have more than WordPress setup into my website
Basic WordPress on the root: http://www.example.com
Another WordPress in an internal folder: http://www.example.com/folder/

When I try to backup the basic WordPress, I see that this backup is also backing up any internal folder including the 2nd WordPress!

Is there any option for the plugin to allow me to select which files/folders to include and which to not include into my backup?

https://wordpress.org/plugins/duplicator/