Go with what the content matches closest to for the classification--the honors distinction will appear on the course number as you noted.
At my college, I had friends take honors general chem since they had AP credit in chemistry (which some schools don't take) but still wanted to meet medical school requirement of 1 year of gen chem. Had they classified it as special studies it might not have been as apparent that they met the requirement.
Hope this helps (and if its any consolation, the verification process will attempt to fix any input errors and or grade mismatches).