It is only the new version (to be deployed in the coming weeks, most likely in January 2010) that markdown is the pivot format and you will be able to use the "latex to markdown" conversion of pandoc to upload texts.
With the present version, the best solution is either:
- Through OpenDocument and upload, which is a pain when you start from lyx, as lyx to OpenDocument does not work well.
- By generating HTML from lyx, displaying it in a browser, creating a new text in co-ment (http://www.co-ment.net/text/add/) and cutting and pasting from the browser to the edition window in co-ment. This is ugly as a method but works well if you don't have images.
or write it directly with your browser
work privately on your text with a few chosen collaborators
or open the commenting process to the public
use comments to improve your document and create new versions of your text
export your text (and all comments) in any format (MS Word, OpenOffice Document, etc.)