The Journal field is automatically set up to work with the Journals term list. This means that the Journals list is updated as you add new journal names to your references, and EndNote will use this list to facilitate data entry by suggesting journal names as you enter them into the Journal field.
The Journal field (in the Journal Article reference type) can be used with the Journals term list to allow for multiple formats of a journal name to be used in your bibliographies, depending on the format required (see Creating Bibliographies with Journal Abbreviations). When the different forms of the journal name are entered into the Journals term list, all it takes to change the format of your journal names in a bibliography is one change in the style used (see Journal Names). All of the appropriate substitutions are made when the bibliography is created.
EndNote includes several predefined journal lists in the Terms folder. If you would like to use these lists, you should import them into your Journals list as described in Loading Supplied Journal Abbreviations.
The Alternate Journal field is most useful when importing or retrieving references from an online source that provides two forms of each journal name (full and abbreviated). By importing both, you can easily update the Journals term list and use the correct form of the name without having to enter it yourself (see Updating a Journal List).
If you do not import from sources that include an alternate journal name, this field is probably not necessary for you to have in your Journal Article references. You can remove it by editing the Reference Types preference (see Customizing Reference Types).