...change the color of your adsense ads directly in the code or is it better to make all new ad units in your adsense account and repaste them into your entire site? I know google doesn't like you to mess with the code once the ads are on your site but, if you only want to change the color, is it a problem?
When specifying custom colors for ads in the Adsense admin system, you are able to type in any hex code you wish. Google have spent ages programming the system to reject any incorrectly formatted hex codes like #ffxx22 They could quite easily have created the system to stop you typing any codes in at all. I think because of this it is absolutely clear that they are perfectly happy with you modifying this to your heart's content, and whether you do this in the Adsense admin system or in the code of your page is irrelevant and can't be detected by Google. Just make sure not to edit any other parts of the code.