Do I have to do anything different for incremental backups?

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I have no problem with full backups. I simply put "MSSQL:" as saveset and "nsrsqlsv" in the remote command field. I setup another client for this machine with "MSSQL:" as saveset but "nsrsqlsv -l incr". Unfortunately NSR complained with message:

Server: servername: saveset of MSSQL: would be specified by two 
clients with the name client-name in group group-name.

If you wish to make incremental backups of MSSQL databases, you need to make a specific saveset-entry in the client definition. So instead of

MSSQL:

You need to enter

MSSQL:master
MSSQL:msdb
MSSQL:database1
MSSQL:database2