First, attach the neck to the body. Make sure it's seated correctly in the pocket and locked down.
Lay a 36" straightedge along the side of the neck, against the edge of the fingerboard, and laying across the body. Draw a line on the body back in the bridge area. Do the same on the other side of the neck. The bridge must be centered between those two lines. The pickups should be too, if you are doing any pickup routing.
Verify your scale length by measuring from the fingerboard-side of the nut to the center of the 12th fret. Your scale length is exactly twice that. Measure that same distance, 1/2 the scale length, from the 12th fret back onto the body and make a mark. That's what we call the Zero Line.
Now, adjust the bridge's saddles until they are almost at the front limit of their travel. With the saddles at that position, the bridge should be mounted with the saddle witness points right on the Zero Line. To get proper intonation, the saddles need to be able to be moved back from the Zero Line 1/8" to 3/8". The saddles will never be moved forward of the Zero Line.
To get the bridge square, first spot, drill and screw the bridge down with just one center screw. Then take your time lining it up to make sure it looks right from across the room. Or you can measure from the back corners of the bridge to, say, the ends of the 12th fret. Get it right. Then spot, drill and install the outboard screws.