Searching for video converter that maintains folder structure
Most decent encoders with watch folder support have an option to automatically encode to the same folder structure that the source came from.  I'd check the listing of any software you are looking at to see if it supports it or try a demonstration copy.  I know that Adobe Media Encoder does.

Beyond that level of detail, this is a product recommendation question which is off topic since software may or may not be available tomorrow and the options for video conversion software change frequently.