In CrackMem, there is an option to wipe the device. I have never wiped my device when doing an upgrade. I think one of the upgrade steps is deleting all applications and data on the device.
Desktop Manager does a wipe before it starts the OS upgrade. It does this after it has compelted the Backup.
CrackMem was written primarily as a support tool and that was why I put in the Wipe Device button. It is also why almost all the buttons have a confirmation dialog so that a supporter can verify that the user has pressed the button required by asking about the confirmation dialog.
I prefer not to wipe when I am upgrading. I just let Desktop Manager do its thing and I end up with a perfectly working phone with all my stuff installed and restored.
If you wipe, then this will not happen. At the end you will have a stock OS with none of your apps and none of your personal data present on the phone. You will then have to do a manual restore (you did do a Backup, didn't you?) and possib;e a Sync as well.
I wipe phones only if I have a problem with either the phone or its OS and I always try without the wipe first.