For most systems, I typically recommend using the primary disk’s full capacity as one partition, C:\, instead of creating multiple partitions/drive letters for end users. As an IT Pro, it makes it easier for me to find someone’s “stuff” if they store their data in a standard location like their default profile location, C:\Users\%username%\. If all of your documents, pictures, shortcuts, Favorites, settings, etc. all live in the same place, I don’t have to go hunting for files when it’s time to migrate someone to a new machine. (Or, better yet, I can automate it!) For the end user, it’s just easier: Most people are used to just saving files to the default locations on their home computers. Any time you can keep the corporate computing experience similar to what people experience at home, it saves you time and money.
However, there are some times when it can be advantageous to create more than one partition when deploying an operating system (OS) to a computer. I know quite a few people who actually prefer that their end users store their data on D:\ so that it can be fully separated from OS and applications on C:\. In the event of an OS crash or malware infection that isn’t recoverable, C:\ can be wiped out and all of the user’s data on D:\ is still there. Personally, I’m not a huge fan of that because it tends to miss application settings, the Registry hive, and other important things a user may miss later. But, to each his own I guess.
I am, however, a fan of separating data from OS and software on servers. I’m also a fan of keeping my virtual machines totally separate from C:\ also. (Those things have this bad habit of filling up disks, don’t they!?!)
How MDT Partitions Disks
The disk partitioning process is a task that is part of each OS deployment Task Sequence. By default, MDT creates a C:\ partition using the full first disk and names it OSDisk. If this default doesn’t work for your environment, it is pretty easy to change.
Change the Default Partition
In the MDT Deployment Workbench, go to Deployment Shares > $YourDeploymentShare > Task Sequences. Find the Task Sequence you want to edit and right-click on it. Click on Properties.

In the Task Sequence Properties, go to Preinstall > New Computer only > Format and Partition Disk.
In the Volume section, you should see “OSDisk (Primary).” Click on OSDisk (Primary) and then click the Edit button. (The Edit button is the middle button that looks like a hand pointed at a document with a bulleted list.)
In the Partition Properties, you can change the Partition name, the size, file system, etc.
For our example, we’ll change the partition size to “Use specific size” and set it to 80 GB. Once we’re done, click Ok.

I don’t want to waste the remaining disk space; so, we’ll add a second partition that uses the remaining space. Back in the “Format and Partition Disk” task, click on the New button. (The New button is the left-most button that looks like a yellow star.)
In the Partition Properties, fill in the Partition name with “Data Disk,” and select the “Use a percentage of remaining free space.” Set the Size (%) to 100. Ensure the File system is set to NTFS and click Ok.
When you’re done, you should have something that looks like this:
If we perform a test deployment, you should get an 80GB drive and a second with the remaining space.
