Do you have your original trim for the rear window? If so, look on the backside of the trim. If the clips were a bit rusted, you'll see a trace of that where they sat against the trim. Lay the trim down in place and mark the areas for the holes. The trim clip should be pretty much bottomed out when installed, thus just a tad lower than 1/16" from the top lip of the clip to the top of the panel. The rear window trim clip kits sold today pretty much suck. They're a tad different than factory as is; when they're securely tightened, they sit hard flush against the body. They sit too tight against the panel for the trim to slide between. When I installed mine on my 69' roadrunner, I installed the clips, then taped in a nylon wedge between the trim clip and body, just to make the clip bow out a bit more. I also secured the screws lightly so there's a little give. I backed the screws with some black ribbon tape/seal as an extra guarantee the screws were not gonna budge down the road.
Good luck