Weapons and Tactical consoles for those weapons is your preference.
I like Engineering consoles with resistances.
Science Consoles and Deflector Arrays need to be those that provide the skill bonus that help your science powers. When in space open the powers tray (P key). Find the science powers you have on the list (tractor beam, science teams, jam sensors, Hazard Emitters etc ) that your science BOff(s) provide, or that your captain earns if you're a Science captain. Left click these powers and you'll see the full details in the right pane. In these details you'll see 3 attributes listed at the bottom. These attributes are the captains skills you can train and are found on science consoles and/or deflector arrays. Pick those that you have listed the most. For example, Jam Sensors, of course uses senors and sensor arrays, so a deflector array that adds these two would boost this power.
I'd say toy around with different configurations as far as equipment loadout goes. My T2 BoP was geared essentially as (off top of my head):
Forward: 2 Dual Disruptor Hvy Cannons + Photon Torpedoes
Aft: Disruptor Turret
Engines: With low speed turn efficiency
Consoles: Tacticals - 1 Cannon, 1 Torpedo
The above IMO is generally what KDF rolls with at the start of T2. It works alright, it's familiar with what you should have at the start. Disruptor Cannons work great once you get past shields. Combine with projectiles, it'll do good. It's a decent all around build, suitable for most ranges, but ideal with mid-long range shooting. Substitute Photon with Quantum for a slower reload but harder hitting torpedo strike. You can't put in cannons to the rear of the T2 BoP, but beam arrays or projectiles can be equipped.
Right now I've switched to and been toying for effectiveness with Plasma weaponry.
The above is a short ranged, hard hitting alpha strike build (for me at least) with DOTs via Plasmas. The Plasma Torpedo is ideal for close range work, especially with High Yield. It creates a targetable, slow moving but utterly devastating High Yield Plasma Torpedo. I strip away shields as I close in range, then, under the mask of cannon fire at PBR (Point Blank Range), I let loose the HYT for the Plasma. I frequently can sneak it in if masked in such a way for massive damage that should kill escorts and science vessels if they have some damage on them already. If not, they have a nasty DOT on them from the torpedo, and not many are geared to healing away DOTs. The aft Beam Array was mostly a PVE consideration with all those shuttles flying about. I'd like to stuff a Torpedo in the aft, not a Plasma. A regular Photon would do, but a Quantum would be nasty. The idea would be to strike from one side (cannons + plasma torp and DOT), turn away from that same side, then leave a photon / quantum for a final insult. I've moved away from Disruptors since I know Feds get alot of quest reward shields that have Disruptor resistances. And those shields are VERY nice to top it off. You get a taste of it once you were eligible for creating a KDF toon.
Engines... I normally favored low speed turn efficiency, i.e. dogfighting. But I noticed that alot of my defeats have been getting myself in such fighting. When letting myself get in such a fight, my situational awareness goes down, since I focus on my nearby target alot. That really exposes me to his buddies, especially if they're newly arrived (more so if that new buddy is an escort). For a BoP, that is lethal since I'll be dead in seconds. I favor fast closing alpha strikes, and get the hell out of dodge. For a BoP captain, the worst thing you can do is "stick around in the melee," leave that for the cruisers (well none for us in T2), Raptors, tank builds. I come in, hit hard, get out of town, get out of weapons range, recloak. Assess the situation, get a target (primarily what is picked out by my team), come back in. It takes me discipline to stick with this. It is VERY easy to get into "dogfighting" mode with your prey right in front of you, trying to turn and escape.
Just as important is your BOff selection, especially as a BoP skipper, which directly plays how you will fight as one. I've always been a damage dealer, so my tactical BOff gets the lieutenant slot (2 skills). Tactical (Lt - 2 skill slots) - High Yield Torp 1 / Cannon Rapid Fire 1. I'm debating getting Torpedo Spread for the Plasma Torpedo, but I'm holding off for now. Science - Tachyon Beam (shield depletion, but it's not working out right like I hoped. Contemplating on switching it for something like Sensor Jam) Engineering - Currently set for Hull Repair, which gets me back in the fight sooner and saves me when me hull got pummeled in a fight. But lately when the damage comes, it comes hard and fast, where hull repair doesn't matter anymore. I'm thinking of getting something defensive or something for escape.
Just my findings so far, but I feel I really need work on my BOffs. It just feels "off" compared to how it felt successful in T1. Regardless, when the end of the PvP match goes (mostly FvK), even though I'm low in levels for LtCmdr, I put out respectable damage.
Tac: high yield torp, cannon rapid fire
Engi: power to shields
Sci: Jam sensors
Hit and run anti escort. With dual cannons and not heavies you need to fight under 5k to be effective, but the overall dps is higher. You can knock out an unsuspecting escort's shields and slam in some torps before he knows what's happening. Engine batteries, jam sensors, and evasive maneuvers for a quick escape if someone tractor beams you. Just have to be careful between battery cool down. Can also solo a cruiser well.