I am writing this post also for personal reference (and currently I am writing in bare HTML since my WordPress installation lacks an updated multilanguage plugin to be able to use the WYSIWYG editor).
I was moving my home server from a slow Raspberry PI to a way faster Cubieboard 2, and got to reinstall Transmission daemon. I needed to change its user tho, because I needed a certain folder to be accessible to it.
So I edited as SU the /etc/init.d/transmission-daemon file changing the transmission-debian value into the username I wanted to use, but I kept getting a (warning) message when trying to start the daemon.
Long story short, here are some tips you have to follow, but first credits where they’re due:
This is the page where I got started the first time: http://www.webupd8.org/2009/12/setting-up-transmission-remote-gui-in.html
And this is a heads up I got while trying to solve this problem: https://forum.transmissionbt.com/viewtopic.php?f=2&t=13964

So, back on track:
1) Make sure the transmission daemon is stopped, otherwise changes you make to configuration files will be reverted to original
2) Edit the init.d starting script changing the username to your wanted username
3) chown the default transmission-debian folders to the user you need:

sudo chown username:group /var/lib/transmission-daemon/info –R
sudo chown username:group /etc/transmission-daemon/ –R

4) If you are importing a settings.json file from a previous installation, make sure to copy it to both /etc/transmission-daemon/ and /var/lib/transmission-daemon/info/ so that both copies are identical
5) You can now start the daemon and everything should work as expected