Nextgen gallerys default to
wp-content/blogs.dir/%BLOG_ID%/files/
if you FTP there and upload files, make sure to go to Manage Gallery and “scan folder for new images”
The media library uses
/wp-content/uploads/
and then folders by date.
When inserting a single image into a page, from the media library/upload will auto link to that image, from nextgen gal will be unlinked.