Backing up the game's save files and ships

For Windows 7 and up, they are in C:\Users\<YourUserName>\AppData\Roaming\CDE. AppData is a hidden folder, so don't forget to enable their display in folder settings. Preferences.txt contains the settings you selected in the game; UserDesigns.txt contains your custom designs; UserRecords.txt contains your records for various missions in the campaign. Mods is self-explanatory, and Backups folder contains previous versions of your customs designs that the game creates.