The management of SQL is often performed by different skillsets so there are tools for each audience. It is not a question of System Center vs Application and Multi-Server Management (AMM) but rather what is your role and selecting the proper tool for that given role. Both tools serve in the management of SQL. System Center is targeted at the IT generalist, where SQL Server tools are targeted directly at the DBA. System Center focuses on end-to-end service management across an organization’s environment. It provides real-time monitoring across the organization. Application and Multi-Server Management is strictly focused on the database and helping DBAs better utilize their resources and make decisions about their database environment. System Center services span applications, the database, the OS, and hardware where AMM is focused on in-depth SQL Server planning and trend analysis.
More info can be found at:
http://www.microsoft.com/systemcenter/en/us/optimizing-sql-server.aspx
http://www.microsoft.com/sqlserver/2008/en/us/R2-multi-server.aspx