I've built a few basses (not Warmoth); maybe I can fill in a couple blanks here. If the neck is not pre-drilled (it's an option), you'll have to align, clamp, mark and drill for the neck screws. Use a drill press if at all possible. If it is pre-drilled, it may or may not be perfect. You might want to shield the cavity with copper foil. Pickups need to be placed and aligned, marked and drilled for mounting screws. Electronics need to be spec'ed, acquired, mounted to the pickguard, wired and soldered. The pickguard needs to be placed, aligned with the neck, the pickups, and the route, then mounting holes marked and pre-drilled. Screwholes for the bridge are usually pre-drilled (another option). Don't forget to ground the bridge before screwing it down. Press in tuner ferrules, and hope the pre-drilled mounting holes match the tuners you have. Attach the neck, install a top and bottom string, double check the alignment, and tweak as needed. You might need to adjust the depth of the nut slots. It will probably want fret leveling. It may want a shim. Use copious amounts of masking tape throughout all of this.
Any "magic" is in alignment (of the neck, bridge, pickups, and pickguard), and final fret finishing.
Lots of details can be found in the Luthier board here, or look for the "basses for newbies" thread on the Basses board.