You are right in what you say about separating the system data and user data, and many experts in SQL Server database design say this is a good idea.

However in practice, most people do not bother doing this.

If you do want to split your system data and user data, then set up the second filegroup as you suggest. Then mark the second filegroup as the Default filegroup (Google can find the right command), and all further database objects will automatically be put in the second filegroup.

If the CREATE statement for a new object explicitly requests it goes into the Primary filegroup, there is nothing you can do to prevent this, but if no data placement clause is given (which is the normal situation), then it will automatically go into the second filegroup.