Backing up multiple instance System Databases with distributed Maintenance Plan
I am not that huge fan of Maintenance plans to use such strategy for Backups.

What suits the best to our environment is using ola.hallengren Backup scripts.

It backups by taking the initial folder as the location define by the user and later it itself identifies the instance that it is backing up and thereafter creates the folder respectively: 

Give it a try , as its simple to execute and easy to maintain.