DiskExplorer (http://hp.vector.co.jp/authors/VA013937/editdisk/index_e.html) is at the moment the easiest way to edit X68000 floppy disk images. Unfortunately it's still not as easy as it should be because the latest version is still in Japanese. To make matters worse, the older version doesn't get along too well with X68000 floppies. You'll still have to download the older English version to figure out what the menus in the Japanese version do.
It's loads better than WinXDF (http://web.archive.org/web/20080117180244/http://xperiment.rainemu.com/) though, that's for sure.
I know this is an old thread, but just would like to update everyone that there is a full english version of DiskExplorer available from the lovely fellows over at GreekROMs.
It is available here http://www.greekroms.net/files/diskexplorer.zip (http://www.greekroms.net/files/diskexplorer.zip)
And mirrored here by me in case that page goes down: http://conradstattoo.i8.com/x68000.html (http://conradstattoo.i8.com/media/diskexplorer.zip)