Is there a way in Commander to have the BarTender Document save after it has been processed?
BarTender 10.1 and earlier
Yes, there are several options.
In the BarTender Command Handler Setup, there is a General tab where you can add miscellaneous BarTender command parameters that are otherwise not found in the other tabs of the dialog. One of the tasks that you can assign is Save Document(s). For more information, please see: Command options - general tab
The second option is to add the command line /S to the print command script that you send as part of your trigger information into Commander. For more information, you can look here: BarTender Document Commands
Lastly, you can use BTXML to invoke the attribute SaveatEndofJob. You can learn more about this functionality here: BTXML Format tag