SCVMM: Checkpoints are great for Reversion but not for Serious Backup
Checkpoints in SCVMM are managed Hyper-V Snapshots. Hyper-V snapshots are block-level at the VHD layer and serve great for development environments that need reversion capabilities but are not recommended in production.
For a good how-to guide for creating and managing checkpoints, you can look at the Technet documentation here:
As I said earlier, this is great for scenarios of testing patches, testing upgrades, or working with App-V/Softgrid sequencers. It does not work if you are trying to attain file-level backup/restoration capabilities.
Checkpoints/Snapshots will not give you file-level restoration capabilities, however. This must come through a solution from the guest operating system. Windows Server 2008 and Server 2008 R2 have built-in VSS-based backup features.
You should use the built-in backup features of the operating system within the guest operating system to do individual file-based backups.
Backup and Recovery Overview for Windows Server 2008
Backup and Recovery Overview for Windows Server 2008 R2
NOTE: If you plan to use checkpoints for virtual machines with SCVMM, you will want to ensure that you have merged or deleted all checkpoints before moving the virtual machines or else you will experience delays when migrating virtual machines over the network (using BITS) or during QSM (Quick Storage Migration.)
Even worse, you could have errors from these timeouts that could also result in potential corruption of the checkpoints\snapshots.