To prepare a bootable CE disk for PC based system, you need to create the partition, format it and transfer the booting files.
CE provides a tool CESYS.EXE to transfer boot sector and copy bootloader to target volume for BIOSLOADER.
The tool is created since CE 4 and unfortunately, it is out dated and only support FAT12 or FAT16.
Modern storage devices have larger capacity and prefer or require to use FAT32/ExFAT.
For CE7, there is a new CESYS platform\CEPC\src\boot\tools\bin\i386\cesys.exe that support FAT32/ExFAT but it only works with the new boot loader framework.(platform\CEPC\src\boot\bldr\)
Refer to http://geekswithblogs.net/KMOS/archive/2011/06/30/introducing-the-new-boot-framework-in-ce-7.aspx for the introduction of new framework.
If you prefer to use BIOSLOADER or still work on a project that is pre-CE7, you could use 3rd party bootsector installer, such as http://www.nu2.nu/mkbt/ to transfer the boot sector.
And the DiskPart.exe utility in Windows can mark a MBR partition as active, more info please refer to http://msdn.microsoft.com/en-us/library/cc770877(WS.10).aspx
There is an alternative solution - use CE to prepare bootable CE partition - a CE version of DiskPart, allows you to create, set active a partition and prepare the boot sector as well, http://msdn.microsoft.com/en-us/library/ee478369(WinEmbedded.60).aspx