In applying the theme itself, there are virtually no differences, since you are importing the custom template (masterpage) in Sitefinity as a Sitefinity template and then you are able to select which of the registered frontend themes will be applied to that template. If you prefer, you can still style your custom masterpage separately, and then just include the CSS rules in the theme that will be applied to the template.
Concerning built-in templates, you have some options of organizing the layout on the template (in terms of column width, size, number). Then you can apply additional CSS to fine-tune the looks, as with any other template. I believe our newly introduced Sitefinity Template Builder
will be of interest to you, please check it out and let me know if you have any additional questions.
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