I'm not sure, but I don't think that's possible. If you have two SCH C businesses, then I would expect you to have two completely separate company files - one file for each business.
All I've ever imported from Quickbooks has been my 3 rental properties (all recorded on one SCH E) and one SCH C business. But if you have two SCH C businesses in one company file, I don't think it's possible to separate them on import. Hopefully I"m wrong and someone else will jump in here.
