Can you tell me if and how did you use the DOIs till now, or are you just starting?
I would recommend using the DOI plugin for DOI assignment – this way the system will be aware/know about the DOIs. Then you can also use the DOI export/registration plugins (Crossref, DataCite or mEDRA), that can help/reduce you manual work a lot.
If you did not use DOIs earlier, you would need to chose a registration agency, and contact them, to get the credentials and DOI prefix.
If you explain me a little bit more about your wishes, requirements, or use cases till now, I can maybe tell more…
Concerning the issue cover page: do you see the cover when you go to issues > future issues > edit issue > issue data ?
It seems like you have this image: http://clinat.indstate.edu/public/journals/1/cover_issue_1_en_US.jpg, which would fit to the first issue i.e. with the issue ID = 1 – and it seems like you have only that one issue, right? Thus I am wondering why the preview contains that wrong cover image name. Would it be possible for you to take a look in the database table issue_settings and tell me what do you see there for all existing rows with the setting_name = coverImage?