Data can be exported from Flex using the Configured XHTML export and imported into the Webonary site. These steps clarify the process for doing this manual to produce sites like those that are currently available.
The xhtml can be post processed. This is often done to replace the homograph numbers with Unicode sub-scripted numbers since the style syntax output from flex does not produce a sub-scripted number (but rather a full size number) -> this is no longer necessary, the importer does it for you!. Another reason for doing this would be to combine the lexical relations of the same type under a single heading. In any case, there are XSLT transforms available including CombineRelations.xsl that performs these operations. Follow the instructions for applying an XSLT.
In addition, rather than uploading with the style sheet from Flex, you may want to use the style sheets that have been custom modified for one of the other sites. One style sheet makes the abbreviations into small caps (pacoh).