Don't pollute vimrc with specific colour settings.
If your only concern is Solarized scheme, that's easy.
Solarized is actually a repo under bundle
if you use PathOgen. So, for your question, just go to Solarized repo, create a branch say "custom" and switch to it, then make any customization as you like.
Another method is to put Solarized directly into .vim/colors
as I do. I made version control for whole .vim
folder with some ignorance. In this case, you can create branch as well, with a big more sweat.