Based on original Windows CE Storage Manager.
Install CAB file and go to Settings->System->Storage Manager
This program allow you to manage your stores and partitions.
You can format and dismount store.
You can create new/delete/mount/dismount partitions in store.
If your partition have FAT file system, you can also format, run scandisk and defragmentator.
On format tool you can select cluster size.
Scandisk can find errors in your SD, CF card.
I didn't test it, because all my attempts to create a lost clusters on SD 32mb failed
If someone know how/can test it, please do it.
Defragementator is very slow, but it works, at least on my 32 mb SD card.
I try to defragment 1 Gb SD and wait during a hour, but it didn't finish it.
I don't recommend to do experiments with your system stores and partitions.
You can create several partitions on your SD, CF card and it works!
I create a four partitions on my SD 32mb card and it works!
I have SD Card, SD Card2, SD Card3 and SD Card4 now.
You should careful use this tool.