Well the case is that Configuration Manager doesnt support patches that require User input and isnt therefor replicated to the Configuration Manager environment. So theese updates need to be deployed in another way, although many customers patch clusters manually so it is not a problem for them, but you wont see the compliance status for thoose patches either. So Config Mgr admins out there keep an eye on this´so you wont miss important patches for your environment.
To find updates that cant be installed with Configuration Manager you can query your SUSDB for patches that require User Input.
USE SUSDB
SELECT SecuirtyBulletin, DefaultTitle, KnowledgebaseArticle, InstallationCanRequestUserInput
FROM PUBLIC_VIEWS.vUpdate Where InstallationCanRequestUserInput = 1
Source of material: http://social.technet.microsoft.com/Forums/en-US/configmgrsum/thread/a4ea7e76-0589-4eb4-a31f-a17b6ab9ea41
If you are installing Configuration Manager on a Windows 2008 box you need to fullfill some prerequsites to install it as a Site System.
I prefferably use ServerManagerCmd to install most of thoose prereqs.
Here are some hint for the IIS prereqs.
IIS Prereqs
ServerManagerCmd -i Web-Server
ServerManagerCmd -i Web-Static-Content
ServerManagerCmd -i Web-Asp-Net
ServerManagerCmd -i Web-ASP
ServerManagerCmd -i Web-Mgmt-Compat
ServerManagerCmd -i Web-Windows-Auth
ServerManagerCmd -i BITS
ServerManagerCmd -i RDC
You also need to add webdav and configure it according to these instructions.
http://technet.microsoft.com/en-us/library/cc431377.aspx
When SP1 for Configuration Manager was released a new feature Called Asset Intelligence was included. With this feature you could set up so you could syncronise Asset Intelligence Data with Microsoft so you got updates from their central catalog. And for that you needed a SA agreement, but as of now you dont need that and the certificate will be posted on the Microsoft website soon.
As soon as it comes out I will post a link to it here, so stay tuned.
Instructions on how to install the Sync Point is found on the link below.
http://technet.microsoft.com/en-us/library/cc161885.aspx

It is closing in now, Microsoft TechDays in Västerås. If you haven’t registered it is a good idea to do that now, and if you are booked and haven’t booked a Hotel that is even a better idea. Great sessions and great speakers is up to come, unfortunately there will not be any System Center Configuration Manager sessions, although if someone is interested in talking about it, I will be there and as always happy to talk about it. I guess there will be some more System Center interested people there so, if you feel that you would like to meet up I can arrange a meeting for SCUG, System Center User Group – Sweden.
If you are interested send an e-mail to techdays[at]scug.se
If you want to sign up to the event you can do that here.