After you upload an OXZ, e.g. beercooler.oxz, you can go to its file page on the wiki by prefixing it with "File:", e.g.
http://wiki.alioth.net/index.php/File:beercooler.oxz.It looks like the below, except you probably won't see the delete and revert actions:
After uploading the first version, I uploaded two more versions of the file using the "Upload a new version of this file" link at the bottom of the screenshot. I kept the filename the same on all three uploads, so it always remained "beer cooler.oxz", no version information added. As you can see in the screenshot, I described the changes in the comment field. Instead of, or in addition to, doing that I think it would have been better to write the version number of the file there. This would show you the OXP version number directly on this page for each version.
The download URL that the wiki creates remains the same for the most recent version, so once you have an URL from the first upload you can keep on using that same URL and always get the latest version from there.
Older versions get moved to an archive, you can see their download URL when you look at the link of the date/time of the version.
The download counter keeps on counting when you create a new version like this. If you instead create a new version with a new filename (e.g. I would have created beer cooler-1.1.oxz, beer cooler 1.2.oxz etc.) then you would get one download counter per version.
It does make sense to keep multiple versions of an OXZ if you want to maintain separate branches, e.g. for different versions of Oolite, or if you want to track download numbers per version.
I hope that helps (and works with the OXZ manager mechanism)
.