Now sinces closed beta ive flown cruisers in with my main engie char. Now that I have the weaver im completely lost on how to out outfit it and which abilities to use. I will mainly use this ship for endgame stf and other fleet actions. I almost never pvp. Any help with how to outfit and use this science ship would be great.

Depends if you're going for PUGS (Pick Up Groups) or with people from a fleet that you know fairly well.

Generally speaking, you can safely assume that other players in PUGs are going to be completely rubbish. If you start off with this mindset, and build to be able to solo stuff, then you won't be too disappointed.

If you're in a fleet, then by all means specialise into a "tank" or "healer" or "crowd controller" or "glass cannon" build. As an Engineer, the Orb Weaver is probably best suited for some combination of those first three.

For a PUG, I'd build for DPS first, and CC and Survivability second.

I posted my Tac Officer's Orb Weaver build here.

An Aux2Bat build going for all-out-DPS is something of an aquired taste though, a more general-use build that won't steer you too far wrong would be:

Universal LtCom (Tac): TT1, TS2, APB2
Ensign Tac: TT1
LtCom Eng: EPTS1, EPTS2, Aux2SIF2
Ensign Sci: PH1
Com Sci: HE1, TBR1, TSS3, GW3

I'd stay with the 2x Quantum Launcher/1DBB fore and 3x Turret Aft setup though.
And remember to bring at least 2x Purple Projectile DOFFs...