For the Journal Abbreviations to work properly, you need a complete set of the journals and their abbreviations in the “journals terms list” in the library selected. See http://www.library.uq.edu.au/endnote/journal_terms.html and the Endnote FAQ at http://www.endnote.com/support/faqs/Styles/faq5.asp.
To underline the Journal names, you need to edit the style to underline them in the Bibliography Template for Journal Ariticle. Select the word “Journal” and then “ctrl+U” or click on the underlined U in the toolbar.