Not 100% what you're asking, but: /usr/bin/transmission-daemon is due to the program being run using the full path, which is legal for any program. it's not an issue at all.
As far as running as your user: transmission-daemon by default runs as a specially-created user called 'transmission-daemon.' this is a common security thing (see below), and isn't necessarily the cause of your problem. I run it as the special user on one of my machines, and it doesn't prevent me from adding torrents.
You should set the config option 'message-level' to 3 and see if the log file provides useful info. My guess is you're trying to save something (the torrent, the target file, resume data, etc) to a location transmission-demon can't write to, because you've changed the default locations for saving these files. If you want them saved to a particular place, you can set up transmission to move the files to a new location when the dl completes, with permissions set up such that transmission-daemon can write there.
Possibly (i forget my permissions-fu) you could add the transmission-daemon user to the $YOUR_USER_NAME group. this will probably allow it to write where you want it to write.
in re the security thing: the idea is that since one use of transmission-daemon is to listen to requests from the internet so you can send download jobs to your computer at home or something, it's an attack target. so in the event that somebody hacks it, you want to be sure they don't thereby control your whole machine. so you make a user called transmission-daemon which can only do a few things like run transmission-daemon. this makes it harder to turn hacking transmission-daemon into full-fledged pwnage.
of course, adding transmission-daemon to your user group will probably make it a lot easier, but whaddaya gonna do?