To facilitate the procedure of creating virtual machines that have aligned system partitions, you can create a template of the aligned virtual machine and deploy new virtual machines from this template.
For example, if you align a disk by following the steps in Section 7.6.4, “Aligning Partitions for Windows Virtual Machines”, then create a new virtual machine that uses this disk, and then install Windows Server 2008 operating system in the virtual machine, you will have a clean Windows Server 2008 installation on the correctly aligned disk. Now you can create a template of this virtual machine and use this template each time you need to deploy a new virtual machine with Windows Server 2008.