In my case I do use the solarized color scheme. Until now I used to override certain color properties in my vimrc. But the number of adjustments seems to grow over time. Especially I tend to adjust colors used for UI elements, e.g. line numbers, highlighted search, highlight groups, etc. Now I asked myself if it makes sense to maintain color settings in my vimrc at all or if I should rather fork the color scheme and merge my changes directly with the color scheme file?
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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.

Billy Chan
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Thanks for your hint. It's rather a general question. I just gave solarized as an example. But I assume I can apply your way of doing things to other schemes as well. Btw. I do use vundle as a package management util. – Saucier Mar 31 '13 at 14:50
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Or you can make custom branch for Solarized repo, and version control /.vim for other things including other schemes. Doing them together doesn't hurt. – Billy Chan Mar 31 '13 at 14:54