I want exactly the same answer. I develop sites in just this way (so do most people I think). So far all I've found is suggestions that the XML file needs to be changed to match my CSS file. This is ridiculous, unless I can generate the xml file automatically.
Dale, I think you need to create the css choices in the Drop down inside the config file as well as add your CSS file. Look at the samples site bundled with the FCK download. Javascript example 14 defines its own custom CSS styles in the style drop down. Custom styles are also applied to core features of the editer tool bar such as Bold for example. See some snippets below. I'm trying to do exactly the same as you so these features will be key for me. Hope this helps.
Re: CSS Issues
Regards
Pete
Re: CSS Issues
FCKConfig.CoreStyles.Bold = { Element : 'span', Attributes : { 'class' : 'Bold' } } ;
FCKConfig.CoreStyles.Italic = { Element : 'span', Attributes : { 'class' : 'Italic' } } ;
FCKConfig.CoreStyles.Underline = { Element : 'span', Attributes : { 'class' : 'Underline' } } ;
FCKConfig.CoreStyles.StrikeThrough = { Element : 'span', Attributes : { 'class' : 'StrikeThrough' } } ;
FCKConfig.CustomStyles =
{
'Strong Emphasis' : { Element : 'strong' },
'Emphasis' : { Element : 'em' },
'Computer Code' : { Element : 'code' },
'Keyboard Phrase' : { Element : 'kbd' },
'Sample Text' : { Element : 'samp' },
'Variable' : { Element : 'var' },
'Deleted Text' : { Element : 'del' },
'Inserted Text' : { Element : 'ins' },
'Cited Work' : { Element : 'cite' },
'Inline Quotation' : { Element : 'q' }
} ;