have you tried
/Applications/path/to/remote/desktop/here
for instance, to start vnc, my remote control solution of choice, i have the following command aliased to "vnc" (so i ssh in, type "vnc", then am set):
/Applications/OSXvnc.app/Contents/MacOS/OSXvnc-server -configoptionshere
my greater point: inside the remote desktop app folder (within Contents/MacOS) there should be an app you can call from the command line in a manner analogous to that which i use above for vnc.