Everything is saved in ".activities" folder under the user's home directory. This means that even if you reflash your device, the activities will be preserved. However, you should create a temporary activity and switch to that one before reflashing your device. Since actman saves the desktop contents whenever you switch to a new activity, after you reflash the device you'll loose the contents of the last selected activity.

If you want to do a backup, just copy this folder (/home/user/.activities) and restore it.