Well welcome to Magento!
First, I would read this PDF from Magento about Designing a theme.
In regards to your question. In your local.xml (app/design/frontend/YOURPACKAGENAME/YOURTHEMENAME/layout/local.xml) you will need to add something like this:
Next, create your custom.css here: skin/frontend/YOURPACKAGENAME/YOURTHEMENAME/css
I would create your own theme (the PDF will help) rather then editing the base/default. The PDF will show you how to set it up.
Word of advice, it will take awhile to figure everything out. I have been working with Magento for 5 years everyday and I still learn new things. I would also learn version control. Version control is your friend and does take a while to figure out now, however you will save yourself time down the road.