There are a number of SSH-based tools available which you can use to script commands to multiple Mikrotik's. You can also implement a system where you have a scheduled script which runs every few minutes or every hour and checks to see if a new script file has shown up. If the file exists, it gets executed and then removed or renamed. With this in place, you can now just ftp files to all of your units to have a global change implemented. In ROS v3, you can have your timed script go get a script file and execute it.
All of this requires some scripting and maybe some coding on your part.