The intonation tool just screws in to the back of the sadles, then you unscrew the sadle lock-down screw and start adjusting, sort of.
The little srews in the bag are lock srews for the trem studs, they are screwed in from under the stud however, so you need to completely remove the studs to fit them. And then you might aswell replace the studs for proper 2LE2B studs...
If this isn't in the manual it's quite bad, Edge Zeros are on the most prestiges now, Ibanez should have updated the manual by now...