If you are using EndNote to keep track of your references for a thesis/article/book you will need to take particular care with the following issues

• If you have multiple papers written by the same author, all author entries will need to be the same. EndNote gets confused if you have a Janet Smith, and a Smith J. A.
• Learn how to use the Groups feature of EndNote X2. This will help keep track of references you need for different subsections of your thesis. You can create Groups that are important to you and click and drag references into these groups. Your Master Reference list still contains the complete listing
• If you are joining separate files together keep all inserted EndNote References unformatted.
  
  
  
  

How to combine separate files to produce one long document with a single bibliography at the end of the document using the copy and paste method or the Word Master Document feature

Copy and Paste method

• Make a copy each chapter to use for your new document
• Using these copies unformat your references: Word > Tools > EndNote X2 > Unformat citations. Save these changes .
• Combine each file in the correct order according to the Table of Contents for your thesis by copying and pasting them into a new document. This can then be saved as a master copy of your thesis
• Using a copy of your final document, Word > Tools > EndNote X2 > Format citations.
• Save your final file with the completed Bibliography

Word's Master Document method

• Create a file that will serve as a placeholder for all the other files that will make up your thesis. The Master document becomes an outline document that you add new subdocuments to it. These subdocuments can be the chapters in your thesis. Save it with a distinctive file name and locate all files in the samefolder!
• With this Master Document open in Word, select View | Outline from the main toolbar in Word. Turn each thesis chapter into a subdocument of the Master Document by clicking on the insert subdocument icon shown on the Outline toolbar below
  
• Insert each chapter in the correct order
• Continue this process until you have added links to all the sections of your thesis

Your Master File will look like this once you have added your subdocuments:

To create the final bibliography when your document is finished

• Start with all subdocuments with temporary EndNote references only. If you have formatted the references
• Make sure you have added the temporary citations to your chapers from one EndNote Library.
• Position the cursor where the bibliography is to be located or create a separate bibliography file and add it to the Master Document file as a sub document.
• From the Endnote X2 tool-bar, click Format bibliography. The bibliography may need to be re-formatted to match the font and type size used in the rest of the document.
• Use the Layout tab within the Format bibliography option to correct any style problems

Tip:

If references are changed in any of the subdocuments, the master bibliography will automatically be updated with the new changes.