As you pointed out, the answer to all of these questions are indeed in the Portal Skinning Guide.  ;)

You may want to change the name of your CSS file from "Skin.css" to "skin.css".  I am pretty sure that a regular expression is used to find that file and import it into your skin.  That being said, make sure that you do not explicitly leave a reference to your CSS file in your skin (HTML) file.  This can cause havok in terms of proper CSS inheritance.

In order to change the default properties of your skin objects, you need to include an XML file.  For a global change, name the XML file "skin.xml".  Then, put something like this into the skin.xml file:

<Objects>
    <Object>
        <Token>[COPYRIGHT]</Token>
        <Settings>
            <Setting>
                <Name>CssClass</Name>
                <Value>YOURCLASSNAME</Value>
            </Setting>
        </Settings>
    </Object>
</Objects>

Now, when you upload or re-parse your skin package, the COPYRIGHT skin object will pick up your CSS class.  The tokens and their appropriate settings are shown at the end of the Skinning Guide document.  For 3rd Party skin objects, you would need to consult their documentation.

Your first skin is always the hardest, because you as the designer will not understand how or why everything fits together the way it does until the first time you complete a skin package the way you want it.  I know this all too well.

I am glad to help.