Most of the pros and cons have already been addressed, but I have a Sci VA who flys in the Prometheus so I'd thought I'd chime in.
First, as other have said, you need to get BOff powers that will help your captain in an escort. Flying an escort is about DPS and moderate surviability. In an STF, for instance, you can sacrifice a little survivability if you have a good team who can pick up your healing a little. In PvE, you can pretty much rip through opponents very easily while running just some healing abilities. In PvP, like STF's, if you are with a good team, you don't need as much survivabilty.
A good basic (and I mean basic) build, you would want your 4 front ports to have 3 cannons or heavy cannons and a torpedo of some kind. Your rear 3 slots would be turrets. I am sure you have played enough to realize that all energy weapons should be the same kind. I would suggest that you spend the C-points and get the "point defense system" that is available on the Sao Pauolo +1 class you can purchace at commander level. The PDS is a very good tool to help you fend off lots of targets (heavy torps included). Just my opinion, anyway
One thing to consider, also, is do you want to do AOE (area of effect) damage or single target damage? If AOE, train your tac BOff's in Cannon: Scatter Volley and Torpedo: Spread. If you prefer single target, than you should be running Cannon: Rapid Fire and Torpedo: High Yield. Other Tactical powers that really help are Attack Pattern: Omega, Tactical Team, and Attack Pattern: Beta.
Some Sci Powers that are good to help you not to pop quickly are Science Team, Hazard Emitters, and Transfer Shield Strength. For Engineering powers, I usually use Engineering Team and Emergency Power to Shields or Emergency Power to Weapons (if I have enough healing). Another that I usually don't use, but is very popular, is Auxillary Power to Structural Integrity Field.
For consoles I generally run the Borg console from "Assimilation", PDS console from the Sao Pauolo Class, three of the tactical beam consoles that match my weapons, and one of the tac consoles that matches my torpedos. For Engineering consoles I like Elecromagnetic Hull Plating and the console that helps Auxillary powers (this one helps your sci powers heal better or hit harder in the case of Subnuc or Gravity Well/Tyken's Rift). If you can afford it, for the remaining Sci console, buy the shield enhancers.
I run my captain in PvP and STF's and I usually do alright using a build like this. As you play it a little more, you might find you like a different set up....Play around with it.
Hope this helps
Edited for grammer and spelling