To type diacritics (macrons etc.) in Microsoft Word:

Click on the Insert tab.

Click on Insert symbol, more symbols

Scroll down until you find the character that you want - like o with a line over it.

Then you can create a short cut so that you don't have to do all of this again.

Click on Shortcut key and assign a shortcut (like alt o).

Now when you want to type o with a macron, you can simply use alt o

Follow the citation format you usually use, but make sure to pair the Japanese with transliteration (romaji) so that your sources can be understood by people who don't read Japanese. Yale has a nice set of examples according to the different formats. 

http://guides.library.yale.edu/content.php?pid=568151&sid=4690137

It looks like this: 

Abe, Yoshio 阿部善雄, and Kaneko Hideo 金子英生.  Saigo no "Nihonjin" : Asakawa Kan'Ichi no shōgai 最後の「日本人」 : 朝河貫一の生涯 [The last 'Japanese': Life of Kan'ichi Asakawa]. Tōkyō: Iwanami Shoten, 1983.