matze-
Sounds to me like you're on the right path.  Be aware that different modules may use their own module-defined CSS so, even if you get things correct at the portal level, you may still have to tweak CSS within individual modules.
 
I'd recommend the following approach:

1. Get a CSS insepctor add-on for your browser.  There are a good number of free ones to pick from for FireFox.  For IE I often use the free debugBar add-in which I've blogged about here (includes screenshots).  
    
   Using your "inspector" tool you can select page elements from your site and see ID values, assigned CSS classes, etc.  A good tool will also tell you where each piece of applied CSS is defined (very useful).  I use such "inspector" tools nearly every day.
    
2. Create a test page on your site with some sample content.  Use the test page's HEADER TAGS to declare your own CSS < style > tags for overriding existing styles.  This will override the attributes defined in default, portal and skin CSS files but will not override inline attributes or attributes defined at the module level (the inspector tool will help clue you in on locating source files for module-defined CSS). 
    
3. Once you have nailed down your modified CSS definitions, roll the changes into the "skin.css" file for your selected skin.  There are other places you could place the modified CSS but, since you are specifically overcoming CSS problems with your skin, defining the modified CSS at the skin level makes the most sense (you'll probably want the same changes if you use the skin elsewhere).

 
Hope that helps.  Good luck!
-mamlin

Looking one more time at IE wd bar I found out that I have to overrride the SubHead class. That can be found in the default.css