Can I create a shopping cart in Shopping Cart Creator, then go into the code to customize it to fit into my current website, or do I have to design everything in scc and scd?

You can make some changes to the css file, but be aware that every time you make other changes with the designer, those changes in that css file will be removed. So the alternative would be to keep a copy of your css with changes, and then upload that separately if you make more changes in the application.

You'd be much better off using the SCD Pro and creating your theme that way so it integrates better. Most all the settings you could need to create your theme to match should be able to be found in the program without having to alter the files manually. Keep in mind also that there would not be much support for your theme(s) if they were altered outside the program since everyone codes differently etc.

Having said that, as Janys said it can definitely be done and I've seen some beautiful designs that people have created by altering the code after they created the base in SCD Pro. Good luck with it whichever way you go.

Also keep in mind that SCD Pro's update soon will bring more functionality to the already pretty featureful program