To control the font and paragraph styles of your reference list there is a menu that you may not know is there. On your Endnote ribbon in Word, there is a small arrow at the bottom right of the Bibliography section. See this screenshot.
Clicking on the arrow opens a window with two tabs. The Layout tab lets you specify the font style and size and also control the line spacing and indents of your paragraphs.
In most this window give you all the control you need, but if you are still having trouble, you might need to check the settings in some other places in Endnote. Here is a post with some more detail that can help troubleshoot.