For my eng slots I run ep2s1, ep2w2. In beta vector, with sufficent engine power, I can hit the defense cap while at half throttle. I use ep2w and direct my excess weapon power to my engines and shields. I prefer ep2w instead of just engines because the boost to energy damage is the better buff, and managing power makes the power I get flexible.
The sci setup is a bit more flexible. The old standby, and likely the most common, is tss1 he2 gw1. I use that most of the time. The others that stick out as useful are any mix of tss, he, and one of polarize hull, tractor beam, tachyon beam, feedback pulse, or scramble sensors (scramble sensors is of no use in STF, but is a very potent ability in other PvE)
I once again match my character. Behold the power of PINK!
For my setup I use Emergency Power to Weapons and Energy Modulation(? the better shield penetration one) on my engineer and Hazard Emitters and Emergency Power to Shields on my science officer.
I also have an engineer on hand who is more tuned towards shield maintenance but I use my "tactical engineer" more often since the sci abilities I have serve me well enough for keeping me up and running.