You can add notes to all of the references imported from a database automatically by using EndNote's Change/Move/Copy Fields function.
The text will be added to the Reserach Notes field of all the selected references.

You can use EndNote's Groups function to create individual groups to house results from each of the databases. See the EndNote Getting Started Guide to find out more about creating groups.
To remove all duplicate references from your library at the same time:
See the video below for more details.
In EndNote Desktop version X7.2 and above, you can share your entire library with up to 14 other people. Check out How to share your EndNote library and the video below.