There's a simpler way to create backups rather than make copies of the SYS directory.
Open Builder and select "File > Backup to Client ... " and supply a name. The resulting XDO file will contain everything needed to restore your Premise configuration. The file includes what you see in Premise Home, Modules, related images, and the current state of all properties. The file is in XML format and, if you're curious, it can be viewed using a web-browser or text-editor.
What's nice about it being in XML format is that the backup file is not a 'black-box' and can be viewed and, in the event of corrupted data, potentially corrected. If you load a corrupted XML file into a browser, like IE, it will halt at the offending line thereby giving you an idea of where to fix the problem. Its appearance seems a bit overwhelming at first but its really not too bad because it is structured data (XML) after all. The chances of needing to fix a backup file are slim to none.
The Premise Server Service also performs periodic backups. Look in \Premise\SYS\Backups and you'll find ten files (backup000.xdo to backup009.xdo). The server saves ten snapshots, from 000 to 009, and then starts all over again. If you restart the Premise Server Service, it'll attempt to load the most recent backupNNN.xdo file. If it fails, it falls back to an older backup.
Another useful thing to do is periodically export the entire Modules section. If you run into trouble during the installation of a Module you can restore the entire Module section to its previous state.
The "Modules" directory that you described is simply a parking lot for Module files (XDO's). It is a 'convenience folder' intended for storing custom Modules in one place. Whatever you park there will appear in the File > AddIns > Modules check-list; however, they are just files on your disk and not part of Premise just yet. Using the check-list, you select the Modules you wish to use, click OK, and then Premise imports them. The imported Module will appear in Builder's Modules view. Now they are part of Premise. To uninstall it, return to File > AddIns > Modules and deselect the Module in the list. This is the 'organized way' of installing/uninstalling a Module.
In practice, you are not obliged to park Module files in the Modules directory. Your Module files can reside wherever you please. To import them, simply select File > Import, navigate to the desired Module file, wherever it resides, and click OK. The Module file will be imported and will appear in Builder's Modules view. To uninstall a Module, just delete it manually from Builder's module. This is the 'expedient' way to install/uninstall Modules.
If you buy into 'organized way', you should resist the temptation to use the 'expedient' uninstall technique. If you delete the Module manually, that nice check-list, in File > AddIns > Modules, continues to show a check-mark next to the Module you just blew away. Now you have the extra step to uncheck it order to restore order to the world.
FWIW, I use the 'expedient' method.
