Unfrotunately I have nearly zero experience with those tools, I just looked up for possible ways to connect it to Confluence and word conversion seemed to be the easiest way, sorry :( Maybe other community members have more experience on the topic though!:)
Unfortunately those files cannot be imported directly to Confluence, you'll first need to convert/save them into Word format, then import that. You can find instructions on how to convert here: http://blogs.adobe.com/techcomm/2012/10/converting-fm-docs-to-ms-word-files.html
WebWorks ePublisher (start with ePublisher Designer) produces old-style Confluence wiki-markup. Make sure this is the format your Confluence content is written in. If you are expecting to use the WYSIWYG editor in current versions of Confluence, ttbomk, ePublisher Designer is not your import path.
Time has passed, which solution did you adopt?
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