Keep in mind that colors may look slightly different for everyone, because of their monitors/TVs and graphic card settings. Personally I use a SweetFX to fix the colors and I haven't noticed a huge difference between CC and game. If worse comes to worse, simply create a 'test' character with different hair/eye colors and once you figure out which one looks best in-game, write it down.
It's almost impossible you cannot notice the difference. The character creator is rendered in the Fade, which has very, very different lighting from everything else in the game.
Unless you've never used anything else than black make up. Cause honestly, as soon as you start messing with coloured make up you really need to adjust for in game lighting. If you don't, your character will come out looking like a clown with neon-glow
This took me like 3 or 4 tries to get right:


The Fade: