There is a new "free" skin object available that is easy to setup and use. You just need to become more familiar with your skin files and your DNN directory structure.
If your going to use jquery, you have to enable jquery in you Host settings. You can find lot's of information on how to do this with a simple search.
Once you have the skin object installed you can add your ".js" files to a folder in your portal root and reference them in your skin ".ascx" file using the sking object. Then it just as simple as using a text/html module to copy and past the remaining html code. This method applies to both javascript and jquery.
http://ultimateskinobject.codeplex.com/ http://plugins.jquery.com/ http://www.dnncreative.com/Tutorials/SkinningTutorials/DotNetNukeASCXSkinning/tabid/504/Default.aspx