[NAME], Keeping separate workflows for different instances of a DB on SQL server is the best approach. Specially in your case where you have different recovery modes set on different instances. You could create a separate policy based on either application e.g. front end, middle ware , back end, logging servers for any application that you have in production, or you could segregate it based on the data type like SQL in one policy, Exchange in one, Linux FS in once and so on.
I'm fairly new to Networker and have a few questions hopefully someone with more knowledge and experience can help me with.   This question is about backing up MS SQL server db's. Suppose there is a MS SQL server with several databases - with some of them in Full Recovery mode, and some of them using Simple Recovery. If I have a workflow that backs up transaction logs only, I end up with failures - because of the dbs in Simple Recovery mode.  The workflow contains many separate/different SQL servers and most of them have dbs set to Full Recovery.  The servers that have dbs in Simple Recovery mode will always show in NMC as failed  (I also have a separate workflow that does full SQL server backups - no problems/failures with that) The way I get around the failure is to create a specific workflow just for the server with mixture of Full and simple Recovery to backup only the (transaction logs for) db's in Full Recovery mode. This works, but I am not sure if that is the right way to handle this situation.  If we have several SQL servers set up this way (with mixed db modes, thus necessitating separate workflows), I would end up with many, many more workflows and managing them and keeping things straight would be far more difficult. Is my approach correct, or is there a better way to do this?   Any input would be appreciated.    
MS SQL server backups