I think that the issues you are encountering have everything to do with using a template driven program that is designed to protect you from the underlying code. One option to consider is to look at other templates, there are a bunch available on the developer's web site at http://www.realmacsoftware.com/rapidweaver/. I personally use Coda, it is available at http://www.panic.com/coda/. It is a really amazing program, but it does require a decent level of familiarity with the code. I am by no means a code expert, however, and I am really happy with Coda, so if you are feeling kinda adventurous and want to give it a whirl, it might be worth a try. Also, a simple book or web based CSS tutorial might help a lot. You could find out where your css file lives and go in and just change the text color, and anything else you want. I don't know how Rapidweaver handles it if an underlying file is edited outside of the program, however, so that is something that could trip you up.
The web site in my signature was built using a flash template system and I am going to get rid of it as soon as I can. I did build http://reframingfamily.com using Coda plus a couple of downloadable scripts for the slideshow on the home page and the gallery page.