[tony_sologubov]

You can use Custom CSS or Color Schemes on production as long as they meet your needs. You can use combination of both + Custom Skin, if you eventually get the design you need.

As I understand your situation, you have several options
1) Keep using Color Scheme you've chosen + add extra CSS rules via (Custom CSS, Custom Skin or completely new module)
2) Wrap up all your design changes into css files of Custom Skin module (or your own one) and disable Color Schemes module at all

Если вам удобнее, конечно, пишите по-русски.