Here are some basic best practices to follow when working with SCCM 2012 collections.(This article copied straight from Microsoft. Here is the original article)
Do not use incremental updates for a large number of collections
When you enable the Use incremental updates for this collection option, this configuration might cause evaluation delays when you enable it for many collections. The threshold is about 200 collections in your hierarchy.
The exact number depends on the following factors:
The total number of collections
The frequency of new resources being added and changed in the hierarchy
The number of clients in your hierarchy
The complexity of collection membership rules in your hierarchy
Do not modify the built-in collections and instead, copy and then modify the pasted collection (Configuration Manager with no service pack)
If a default collection (such as All Desktop and Server Clients) does not meet your business requirements, do not modify the collection. Instead, copy and paste the collection, and then modify the new collection. This practice helps to troubleshoot collection queries and safeguards against the possibility that future upgrades might overwrite and change the built-in collections.
In Configuration Manager SP1, the built-in collections are read-only and cannot be modified.
Make sure that maintenance windows are large enough to deploy critical software updates
You can configure maintenance windows for device collections to restrict the times that Configuration Manager can install software on these devices. If you configure the maintenance window to be too small, the client might not be able to install critical software updates, which leaves the client vulnerable to the attack that is mitigated by the software update.