Yes, you should use DeepMeta for everything except resubmits, which it can't do because the API does not include that functionality.
I'd recommend you start over - finish the uploads you have done via the website, then do a full fetch from DeepMeta (Ctrl+F5, or menu option iStockphoto/Fetch ALL data from iStockphoto).
In future, keyword, add MRs, etc. first within DeepMeta, then upload from the program. You can make changes from DeepMeta too.