For some upper level research papers, you may need to create bibliographies that separate out primary and secondary sources. Zotero doesn't have this feature in it. But Endnote does! Options:

1. Use Zotero 100% of the time for footnotes, but manually build your bibliography from Zotero using a combination of tags and the "Create Bibliography from items" option.
2. Use Endnote 100% of the time (note that you need to manually insert footnotes separately from citations, which is clunky for Chicago citations)
3. Use Zotero for footnotes, export to Endnote, and use Endnote for your bibliography. 

Write and insert footnotes as normal

1. See the Zotero research guide for help doing this
2. As you add items to your Zotero library, either tag items as "Primary" and "Secondary", or add them to different folders
3. These footnotes will update based on changes to your main Zotero library

Manually create a bibliography

1. Create two different bibliography headings at the end of your paper, one for Primary Sources, and one for Secondary Sources
2. In Zotero, select Primary sources only (either by clicking the tag, or going to the relevant folder)
3. Right click those items + "Create Bibliography from Items"
4. Select options:
   1. relevant citation style (often Chicago - full note)
   2. Output mode: Bibliography
   3. Output method: Copy to clipboard
   4. Hit OK
5. In Word, Paste the Bibliography you just exported under the Primary Source heading
6. Repeat for Secondary Sources
7. NOTE: This bibliography is NOT CONNECTED TO YOUR FOOTNOTES. It is also NOT CONNECTED TO YOUR MAIN ZOTERO LIBRARY. If you make changes elsewhere, they will not show up in this bibliography. You will need to update this bibliography manually.

Insert citations

1. Manually add a footnote (Command+Option+f on a Mac; Ctrl+Alt+f on Windows)

2. Use the Endnote toolbar to insert a citation in the footnote

Once you've added all footnotes...

1. Categorize References > Configure Categories...

2. Drag and drop citations onto the Primary Sources and Secondary Sources options in the left hand panel. You can also rename these categories, or add other categories as necessary. 

Most research databases allow you to export files of saved records that EndNote can then import. The exact steps may vary from database to database but here are the basic steps. (For ArXiv.org, please follow these separate special instructions.)

1) Start in the research database of your choice

1. Open the research database and begin searching
2. As you find relevant sources, mark them or save them to a folder if possible, however that database allows you to save items
3. When you're finished searching, go to your list of saved/marked records and find an Export, Save, or Download option
4. Many databases will name EndNote as an export option, but if yours does not, select RIS, BibTeX, or "Generic bibliographic management software" options. EndNote can read any of those formats.
   NOTE: Whenever possible, select a "full record" export, since that will capture more information, including the often-crucial "short title" for journals.
5. Save the resulting file to your computer.
   NOTE: If your browser opens the file rather than saving it, use the "Save page as" feature in your browser and save the file with a .txt ending.

2) Continue In EndNote

1. Click the "File" menu and select "Import"
2. In the Import box, navigate to and select the file you just downloaded and click "Import"

See below for ways to add PDFs to your library

This is an ADVANCED skill. Expect this to TAKE TIME.

Step 1: Write using Zotero

1. Write your paper in Word, using Zotero. Insert footnotes as normal.

2. When you're done, create a Bibliography as normal. 

Step 2: When you are 100% sure you're done writing, insert citations using Endnote

1. Make sure Endnote is installed, set up, and open. Refer to the main Endnote guide if you need help with that.

2. In Endnote: Find all of the citations you want (you can use the Zotero bibliography you created above as a guide), and highlight them.

3. Tools > Cite While you Write > Insert Selected Citation(s)

4. You may need to click Bibliography > Update Citations and Bibliography

5. Then, Categorize References > Configure Categories...

6. Drag and drop citations onto the Primary Sources and Secondary Sources options in the left hand panel. You can also rename these categories, or add other categories as necessary. 

7. Once you're happy, you can delete the Zotero bibliography you made as a reference for yourself.