Cite While You Write™ always creates the reference list at the end of the Word document it has formatted. If you do not want the reference list to be at the bottom of the document, for example before appendices, there are a few ways to go about it.

When the Instant Formatting feature is disabled (Off), cut and paste the reference list where you want it.
When the Instant Formatting feature is enabled (On), select the entire reference list and use the drag-and-drop method to move the list where you want it.
When you are completely finished with your references and reference list, decode the document (in Word, go to EndNote tab > Convert Citations and Bibliography (PC) / Tools (Mac) > Convert to Plain Text, then insert appendices or the content you want after the reference list.

Screenshot of EndNote in Word with Instant Formatting feature