My advice is to keep things simple. Worry about UI, how the user will interact with data, not colors/borders/line-height etc..., and slowly add colors and style.
For colors you can use Kulor, it's Adobe's application to coordinate colors. What I have found is that doing little changes at a time, day by day, instead of working on a whole design at once makes managing themes easier.
Otherwise I tend to get OCD about everything think and unless you are a designer that really isn't your role in the long run as there is usually a designer and developer for each project.
So to sum it up use the scaffolding methods to get you started with tables, and when you have got most of your app up and going start to clean it up with divs and proper css layouts through small iterations. I think most developers keep things simple with colors and realize that it's not our role to go crazy over it, although we do, and always keep in mind that unless you are both a designer/developer someone else will probably come along later and make everything look much better.