First of all once you have transmission running you can access it via a browser by going to :
http://<ip.address.of.osmc>:9091/transmission/web/
Its basically utorrent on the browser, and you can set up your download location there as well in the options.
The default skin is crap though, but there is a way to change it easily. If you see this post here:
…all the way at the bottom i’ve posted the new skin and a link to the install script.
You just have to download the install-tr-control.sh file from github, put it anywhere in your pi, and run it. Then select to download the Latest Skin from the menu and refresh your browser page to get the new skin. (you might need to do the checkup things it has there as well, like point to your transmission folder, its in the default place the installer said…but i set it up just in case)
In the options you can set up your download location.
Since you have 2 usb disks you might need to figure out the names first. In the console type: df -h
You will see something thats starts with /media and then the name of your hard disk
Just make a folder there called Downloads or something and in Transmission options put that directory name there. You can even make other directories and when you download something change the path to whatever directory you want on the torrent popup window before saving the torrent., for example: /media/NetHD/mp3s
ps: when you download a torrent, the details are hidden, there is an arrow at the bottom right corner…press that to expand the details tab.