Have you ever used a technology for years and suddenly found an awesome hidden feature? This has happened quite a few times to me such as here or here. This post marks another one of those experiences. When you first load machines into Server Manager (like you did in the Best Practices post), you likely freaked out! Dozens of servers were marked as offline and hundreds of services were stopped/disabled.
Most of these will be false alarms. Under Manageability, you will likely see 2008/2008R2 servers that do not have WinRM installed and configured. If you have 2003 boxes still around, you will see errors with them as well. Services errors will mostly be those that are automatic but stop until they are needed (ex: Microsoft .NET Framework NGEN or Software Protection). Any legitimate issues should be resolved now.
To get rid of the remaining Server Manager errors, you will need to exclude and filter Server Manager. Select the category with the errors. In the top of the window, you will see different methods of filtering. For example, I am filtering out the Software Protection service from the All Servers group.
Continue filtering either servers or services until you are at a clean environment! From here, address future alerts or exclude them from display. And that is your Server Manager Quick tip! Are you using Server Manager yet?