The bit I am pointing at is in the bottom of the guide
For that SECOND release, edit the RELEASE on the normal RELEASE editing page. On the TRACKLIST tab you can shuffle your CDs around and set a different order
Those arrows let you set Disc 02 as Medium 2
Looking at your screenshot, I think your discs will at least appear in the correct release now, and you may have to shuffle the order afterwards. (Something a little weird may be happening on that Merge Releases page… something I bypass by just setting my medium numbers before clicking the Merge Release)