I'm not aware of any Steam-related issues with the Skirmisher and I'm pretty sure it is being successfully used by at least a few Steam-users.
The Skirmisher itself doesn't need to locate the Nexus installation, as it itself resides in the Nexus installation folder. For Steam, that path should look like this:
<Your-Steam-Path>steamappscommonnexusI'm not sure, if the last folder is actually called "nexus" or something else, as I don't have the Steam version, but it should be named similar. It is possible the installer doesn't find your Nexus installation, especially in Vista or Windows 7 (although I personally never had a problem with that). Instead you can download the
ZIP-version of the Skirmisher (update
here) and manually extract everything into your Nexus installation folder as mentioned above. Start "Nexus Skirmisher.exe" and it should work just fine.
As for the missions not showing up: they don't show up directly in the modifications menu of the launcher. They only show up after starting the actual mod you created the mission for. Per default that's the "NEXUS Skirmisher" mod included in the above download, so choose that in the modifications menu and you should see your missions ingame. If the "NEXUS Skirmisher" mod doesn't show up in the menu, then something went wrong with the Skirmisher's installation and you should reinstall or manually extract the zipped version to the correct folder.