Mostly you might have created those Sites with Related Settings -> Refer Default Settings. To confirm it please edit a specific site which you would like to associate and check it.
Refer here to know about What is Refer Default Settings and others . Please note As per design, Sites created with Refer Default settings will not be listed in any configuration page.
If yes, please goto Admin -> Technicians and Edit the specific technician and enable “Add this technician to ’Default Technicians’ list”
This will associate all sites äutomatically which are created under Refer Default settings.