That "Custom CSS" box in my opinion is one of Tiki's most valuable assets.
The first reason is, it acts as a CSS over ride, so when you upgrade your tiki installation in the future, your mods won't be over written as they would be if you made mods in your CSS files directly.
Also, for non techies like you and me, it's much easier to apply the modification in Custom CSS than rooting through the CSS files on the backend.
se7en, if you want to customize your installation even further I'd highly recommend getting to know your code inspector. It's an invaluable tool for finding the areas in your theme and changing colors, fonts, and much more. Then you can manipulate the settings for your application and apply them in your CSS Custom box in Themes.
Here is what I am talking about, personally I love the Mozilla Firefox inspector. If you have Firefox, go to "Tools", then "Web Developer" then "Inspector". You now have a visual behind the scenes look at all of whats going on for the page you activated the inspector on.
If you want to zero in on a particular area of your website, click on the area, then activate the inspector, and it will zero in on the area you clicked on. Then see over to the far right column of the inspector, and you can play with those settings in real time and watch your page change as you make the changes, don't worry, the changes will go away when you refresh the browser.
Here is a tutorial on using the inspector at https://developer.mozilla.org/en-US/docs/Tools
If you intend on modifying your website it would be good to study that page, and just play with it and experiment. Personally my limit is changing area fonts, colors, etc. I come back here and ask for major modifications and a few of the guys here, Rick and Gary and Torsten who are typically very helpful in the modification of themes, aren't too far away to answer your questions, or sometimes they even supply some code for you if they have the time.
Now all that being said, I would highly recommend that you set up a second mirror site of your real installation if you have not all ready, and make all your modifications on that site first, then after you have determined the mods are successful, you can then apply the same mods on your live site. The less you change and flip and modify on your live site, the better. At least that is my superstitious opinion.