Basically what Chick said. I'd first measure the bridge and mark on it the centreline. Bolt the neck on, and run string from the two E slots down the neck to the bridge. You can fit the two E tuners on to help hold the string. The trem block on the bridge will limit the bridge placement anyway, so it can't go too much fore and aft or sideways.

Move the bridge sideways until the two strings are running nice and parallel to the edges of the neck, then mark the two sides of the bridge and the centreline lightly onto the body with a pencil. I'd then position the bridge fore and aft so the trem block is in the middle of the trem cutaway. Again mark this on the body and then measure the scale length from the fretboard side of the nut at the high E slot to the high E saddle. The official scale length is 648mm and with the high E saddle adjusted fairly well forwards (but not quite all the way, you should measure 648mm. A little bit either way is OK as you will fine tune the saddle position when you finally get to intonate the guitar. The other saddles should end up 'behind' the High E saddle as they need slightly longer string lengths to intonate properly.

If you can do this with no issues, then mark the bridge screw hole positions onto the body. If you are unsure, come back to us with some photos and your measurements.