The big advantage to running out of your deck is that you know you have no recording if you have no meters. If you are out of the pre and the deck dies, you'll still have pretty blinking lights, but no recording.
The big drawback running out of the UA-5 is that all the analog outs are controlled by the headphone volume knob. Change the knob and the meters are no longer accurate.
FWIW I run mine off my JB3. That also made the initial calibration easier too. I just recorded a 3db constant tone with cool edit then put that file on the jb3.
JAson