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 [...]

From DNN 5, a skin is an extension
The special status of skins has changed; a skin is an extension now in DNN 5, just like anything you install to extend DNN.
Width DNN5 skin as extension we have lots of benefits.

We can use one installer for all extensions

Skins and containers can be package on a single [...]