The first time you convert files for a project, if you intend to use CSS, probably you will want DITA2Go to generate a new CSS file, so you can use a style sheet that contains the equivalents of your format settings. You should also specify a name for the CSS file (see §31.4.2 Designating and locating a CSS file); for example:
[CSS]
UseCSS=Yes
WriteCssStylesheet=Once
CssFileName=MyStyles.css
When WriteCssStylesheet=Once, DITA2Go generates a new CSS file, but only if no CSS file of the same name (in this example, MyStyles.css) already exists in the project directory. This is probably the best setting to use in most circumstances; you can leave this setting in place, and any changes you make directly to the CSS file will be preserved the next time you run the conversion. On the other hand, changes you make to formats will not be reflected in the CSS file.
Force a new CSS, update CSS from formats
To force DITA2Go to generate a new CSS file, overwriting any existing CSS file of the same name in the project directory:
[CSS]
WriteCssStylesheet=Always
If you never make changes directly to the CSS file, you can let DITA2Go generate a CSS file each time; then any changes you make to your formats are updated automatically in the CSS file.
If you make changes directly to the CSS file, to prevent your changes from being overwritten, for subsequent conversion runs you must change this setting to Once or to Never:
[CSS]
WriteCssStylesheet=Never
Styles based on configuration settings
You can have it both ways, by specifying CSS settings in your configuration file for particular formats; see §31.8.3 Overriding styles in DITA2Go-generated CSS files