Hi Philip,
As per your Query:
1) What is best practice to backup these changes. Is it using the central configuration manager option?
Solutions:
If you are changing any thing in Services then it is better to take the backup in terms of Database backup of CMS/AUDIT and BIAR Backup + FRS Backup before applying any changes in the services. Please create a documents regarding changes of Configuration before and after.
2) When apply service pack updates are changes done overwritten e.g. if create extra services, split aps or tewak memory parameters are these overwritten when apply sp update.
Solutions:
If You are applying any patch then Best Practices is to take the Backup of old Configuration Using Data base backup of CMS/AUDIT and BIAR Backup + FRS Backup, but after applying the new Patch it will not hamper your "Job Server" Setting in Central Management Console it will remain same but for best practices take the screen shot of old configuration and then recheck it.
Hope this will help you as well.
Thanks,
Daya