I usually just stick on its tail and plug it with Disruptor fire continuously. It takes down the shields and disables it with out too much headache (granted, I play on Easy). My pet peeve however, is with the wide cannon placement on the Ulysses, which makes converged fire on fighters impossible. I'd prefer to use a Valkyrie instead, but A} you can't customize your craft or loadout for that mission, and B} the Advanced Disruptor can ONLY be mounted on the Ulysses and was pretty much created by

specifically so this mission wasn't impossible to complete. However, making that weapon widely available in later missions would make some of them too easy, thus its use was severely limited. I would have liked to be able to load out the Herc or Valkyrie with it.