skin.css is related to the skins that are in the skin package...
Portal.css - DNN allows you to have child portals and multiple websites under each database.
When you first install dnn - there is Portals/0/portal.css - and that's the core DNN coding for all the 'business look and feel' - I call it that because it controls the fonts that hold the structure together. Thngs like the control panel, fonts that make up the command links, the admin settings, things that really don't need to have 'design management' if you get what I mean.
And, you can put in classes using the Admin/Settings... scroll down the bottom the CSS editor - that's actually writing to the Portal.css file sitting in that portal.
If you had other websites attached to you DNN build, each one would have a Portal.css file - becuase as administrators, we can go in and modify CSS elements of each portal, indpendently.
Some people like to control the lot and I say - good luck to them- If you need to do something that is a once off customised and streamlined site that required precision from A > Z - then you modify the Portal.CSS file.
Skin.css - that's required in each skin to customise it further..
I'll explain in a little more detail here -
Cascading Style Sheets - they have a hierarchy of order -
The outermost has the least control, the innermost or closest CSS coding to the actual html reference - has the most control, and that should help you understand how the DNN hierarchy works too.
The skin.css file controlsl all the global elements pertaining to that skin set.. DNN skins automatically pick that up - it's part of the skinning engine infrastructure.
However, you can customise the skins more by putting in a skinname.css file - eg... homepageskin.ascx would have a homepageskin.css file with some customisation - things like... menu colours, background colours - whatever, so anything you want that is specific to that skin only, it will be picked up BEFORE skin.css, and what is not found in skin.css will be picked up in Portal.css.. and what is not found there is picked up in Default.css and you might wonder why so many files - some people dont' like this and think we should have just one css file for everything... but from my experience, I've found that very few people want to get involved in the skinning of the whole application.
What I suggest you do is copy the skin and rename it, then copy the skin.css file and rename to the skinfile.css name and make all your changes there - don't touch the portal.css file unless you want do something to affect the whole site.
Does this help you at all?