It is advisable to have only one EndNote library.
When you are merging or combining EndNote libraries - you are transferring the references from one library into another. This also imports any attached files.
Open the EndNote library that you want to be your main library or create a new library where all your references are going to be transferred to.
Click on File - Import - File
Choose the EN library you want to import into your main library.
Select EndNote Library from the Import Option drop down menu.
Choose to import all references or discard duplicates.
Then click on Import.
You can also select and then copy and paste references from one library to another.