Just did the switch from Sick(Beard|Rage) and liking Sonarr so far!
Is there a way to override what the default directory Transmission downloads files in?
This question will follow for NZBGet as well, however I dont have Usenet yet…
PS: This is the 5th time I was about to post a message and found my own answer hidden under “Advanced Settings” 
This one seems to stump me though
You’ll have to change the path in Transmission, but you can change the subfolder name that Sonarr will tell Transmisison to use in advanced settings.
With advanced settings on, I can see the following:
Name
Enable
Host
Port
Url Base
Username
Password
Category
Recent Priority
Older Priority
Use SSL
Not seeing where I can change the Subfolder, but maybe I am missing something…
Its Category - its a bit of a hack because Transmission doesn’t support categories (except on OS X), so we opted to make them all the same and use a folder and called it Category to match the other download clients.
Hacks I am happy with / can work with. Just didnt know the Hack -> What I wanted conversion code 
Cheers!