The Chemically Significant Text (CST) field is especially for that purpose. There is a switcher option available on the Configuration that controls whether the  CST only records should be autoregistered or not. If the records fall to the Staging area with "UnknownCST" status message, they can be registered easily from there (Submission page).  If the CST is present in the Chem. Sig. Text dictionary (Administration page), the record will be always autoregistered.

CSTs can be used also for the user wants to register the same structure but as different compounds (receiving two different parent IDs in the database). If the structures of two compounds are the same (or empty), but the CSTs are different, then these compounds are considered as 2D matches (not as duplicates).