Citation plug-ins show up as either separate tabs along the top of your documents in Word or under the References tab. Citation plug-ins allow you to insert citations as you draft your paper and they also allow you to insert a formatted bibliography at the end of your work.
Mendeley's citation plug-in usually appears under the References tab in Word. You will need to set your citation style as APA 6th from within the desktop client before you start inserting citations. To set your citation style, go to the View menu from within the desktop client. (See picture below).
To insert a citation in Mendeley, look under the References tab and click Insert Citation. If Mendeley is not open, clicking Insert Citation should prompt the desktop client to launch. It may also prompt you to login to Mendeley with your username and password. You will see a search box, or you can click Go to Mendeley to scroll through your citation library.
To format your references, position your cursor where you would like to insert them and click Insert Bibliography. Citations used in your manuscript will then be formatted and inserted on your references page.
Zotero's plug-in will typically install a tab in Microsoft Word's task bar along the top. You do have to open your Zotero desktop client first before you can insert citations into your Word document. When you click on Add/Edit Citation in Zotero, a red search box will pop up. If you know any details about the reference you want to insert, such as author name, you can start typing it into the box and Zotero should start pulling up a list of choices that you can click on and insert in your paper (see first picture below). If you would rather scroll through your Zotero library, you can use the drop down menu next to the Zotero icon to switch to classic view. From the classic view, you would then click on your desired reference and click the OK button. (See second and third pictures below).
When you have completed your manuscript, position your cursor where you would like to insert your formatted references and click Add/Edit Bibliography. Zotero should insert the formatted citations used in your manuscript.
EndNote has a couple of unusual differences from Mendeley and Zotero.
For the EndNote plug-in to work correctly, all other Word add-ins must be disabled. To disable or enable Word Add-ins, click on File, then Options, then Add-ins, then Manage Word Add-ins, and click GO. Unclick the boxes next to any other add-ins you have running and click OK.
EndNote will insert a fully formatted citation and bibliographic entry at the same time. If you find this distracting, you can disable instant formatting. To disable, click on Preferences and unclick the box for instant formatting. At that point, EndNote will insert unformatted or temporary citations. Temporary citations will have "curly" brackets around them. When you are done, you can click "Update citations and bibliography" to change all the temporary citations to final citations and insert a formatted bibliography at the end of the manuscript.