I would definately put them on your closed loop pump. A TUBV/DUBV allows you to remove parts of your plumbing without having to move anything or twist the pipe (compared to regular threaded connectors). They are definately better.
So yeah, put one on the input of your pump and one on the output. You'd be better off if you put one on every bulkhead, but thats expensive (might as well do it right though, eh?).
I'm going to be spending about $120 on DUBV when I setup up my 120g. Lowes has them cheaper here than most places online do.