For EndNote to accurately use the abbreviated journal names in your bibliographies, it is important to be consistent when entering different formats of a journal name. The first column should always list the full journal name, and subsequent columns should store consistent formats of abbreviated names. See Important Points About Entering Journal Names.
Journal lists are updated automatically, from the Journal Article and Electronic Article reference types, unless you have turned off the preferences to update lists (see Term Lists Preferences). When journal lists are updated, the entry in the main Journal field goes into the first column of the list (Full Journal) and the journal entered into the Alternate Journal field goes into the second column (Abbreviation 1). Be consistent when entering data into these fields so that the Journals term list will be updated correctly. Note that if the name entered into the Journal field exists in any of the columns of the Journals term list, it is not added again. EndNote tries to avoid duplicate entries in the Journals list.
If you have turned off the preference to automatically update the term lists, you may manually update the lists as described here. When you are manually updating Journal lists, you can choose which columns in the list are used for which fields of data.
To update a journal term list:
Open a library and select the references from which you would like to update the Journals term list. Alternatively, use the Search command to find only those references that you would like to use.
From the Tools menu, select Define Term Lists, and then select Journals.
Click Update List.
Select the fields from which EndNote should extract the journal names. If importing from selected references, check the Update from Selected References option.
Click OK.
When the importing is complete, you will see a column of journal names listed in alphabetical order.