I am putting an addition on the back of my house. There is an upstairs balcony where I need to wire 2 sconce type fixtures on either side of the doors, a ceiling fan in the balcony ceiling, and an outside receptical. The inside walls and soffets are open at this point. Can I use standard metallic or plastic boxes with waterproof covers? I would rather not use surface mount waterproof boxes.

Personally I would use metal boxes, plastic is fine for corrosion, but in time may get stripped out. Then use the weather proof covers, If leaving a cord plugged in, use the "Bubble cover that allows closing cover with plug inserted.
Don't do surface unless you absolutely have to. I would use smurf(ENT)over romex if budget allows. Allows running additional wires in a future expansion.