Thank you so much, comrades! I am feeling pretty comfortable with linux mint, and now would like some suggestions for some absolutely necessary FOSS or free license software for the OS. So far I have the standard, Firefox, ThunderBird, LibreOffice, yada yada. Thank you again to everyone on the linux comm! 
I've had no issues saving to same folder as source when doing batch transcoding queues on Arch Linux. As long as the input and output files does not have the same filename it's fine.