Assuming that you have created MyTheme and theme using Style Switcher.
Step 1
Create MyTheme.custom.css in \Portals\_default\Skins\Tahoe\Resources\css and write all your overwrites / customization in it.
Step 2
@import MyTheme.custom.css in MyTheme.theme.css
Note: You will have to repeat step #2 if you make any changes to the theme using Style Switcher