Only the user running the commit changes routine can be logged into FIMS. If you are getting a "Database in Use" message, there is another user logged into FIMS. Have them log out of FIMS or disconnect them from the server using the server tools.
Once they log out of FIMS, the process will continue automatically. It is best to send an email or communicate that you will be committing changes to staff before starting the process.
Some foundations will run the commit process from the server so they can disconnect everyone but themselves more easily.