I was able to specify both credentials when I first attempted to add the second domain because it had a different user name. However when attempting to add the domain to the management group it would never show up since I assume because the NETBIOS domain was the same as an existing domain already in that mgmt group(possibly an issue with the way this data is stored in the db?). I don't think the credentials play a role in this procedure however I still tried adding the credentials using the UPN format like you suggested in which it presented me with a warning and asked me to specify the Pre-Windows 2000 format which I did and it entered the credential properly.
Besides this one issue, all other domains work fine. We have about 24 different domains total and fortunately all but this one have had unique domain names for both formats.
Currently all domains/wsus servers are in one management group and I use one or more automation server per domain.
I use the default credential ring and have one credential per domain added to it.