Alter-Ego migration parameters are stored in the settings database. The contents of the tree -- all computers and groups -- and the settings database can be saved to a single .AES (Alter-Ego settings) file. This allows administrators to save progress on a partially-configured migration, etc. As settings and computers/groups are intertwined, there is no way to save them independently.
To save the current settings, from the main console menu, click File -> Save Settings. If you have not already saved, you will be prompted to enter a filename. If you have already saved once, the existing settings file will be automatically overwritten. To choose a new filename, click Save Settings As... instead.
To load a previously saved .AES file, click File -> Load Settings and select the file you wish to load. Loading a file will replace all existing computers, groups, and settings in the current tree.
Settings files are given a version number based on the version of Alter-Ego with which it was saved. When loading a previous saved file version, any new options will be set to the default values. A list of options that have changed between save file versions can be found here.