A good friend of mine and fellow Irish System Center MVP Paul Keely has taken the time to write up an excellent guide on SQL 2008 R2 and System Center that will help you make design decisions for your deployments.
From the description:
This is a guide to help you make design decisions and maintenance plans for SQL Server 2008 R2 to support System Center 2012. In the guide you will learn to make server and instance specific changes to support SQL server for the different workloads that System Center requires. We will look at the install requirements per product, what we need to move the data bases and how we should back them up.
Paul has made this guide available on the Microsoft TechNet site and it can be downloaded from here:
He will be refreshing this guide to take into account SQL Server 2012 with System Center in the near future but until then, I'd highly recommend that you take advantage of yet another excellent FREE resource that the System Center community has made available to you and download this today!