General speaking, when you click "Apply" button to commit the operation on Partition Assistant. The operation will be completed under Windows Mode. As below:
However, some operation could not be completed under the Windows Mode, such as "Shrink system partition", "Clone System Partition" or some live applications(include page file) are running on the partition which you want to resize. The target partition could not be locked; therefore the operation will be completed under the boot mode (Partition Assistant PreOS Mode).
Sometimes when you face some error code like error code 36, 12, 1004, you need also completed the operation under the PreOS mode.
Manual start Partition Assistant PreOS mode:
In order to make process running under boot mode you should holding down "shift" when you click "Apply" on the toolbar, and then it will commit the operation under PreOS mode.