It depends on the model. For the 1701-C, I'd put together the saucer and secondary hull and putty (always putty those gaps) them up. But I'd leave the nacelles off because they're pretty close to the hull and would make it difficult to to paint certain parts.
So put together as much as you can minus stuff that looks like it would make things a hassle. For the 1701-D...I'd attach the nacelles, but keep the saucer and star drive separate until I'd finished painting the engineering hull. Then put them together, putty, sand and repaint the sanded area.
Another tip: sand off the raised panel lines. They're out of scale and clash with the wallpaper decals included in the kit.
I don't prime. Never felt a need to, though I handbrush enamels. I suppose I might do it differently if I airbrushed acrylics.