Steps to create skin files and use on asp.net
1. Go to solution explorer  and right click on the website node.
2. Choose “Add ASP.NET folder” and click  ”Theme”.
3. You will see new folder under the App_Themes folder. You will place all the files for that theme on this folder.
4. Create skin files and dump all css [...]

With the introduction of skin as a extension on dotnetnuke 5.x its easier to package both skins and containers on a single installation file using manifest file.
On dnn 4.x versions and previous version it is also possible but differently.
Steps to package both skin and container file on a single installer.
1. Create different zip files for [...]