Pop the hole last
Lots of good ideas on installation of NMO mounts in this thread. I didn't see my #1 rule of thumb mentioned.
Run a cord or strong string FIRST along the path you are going to run the coax.
Then pop the hole in the roof or trunk lid. Then pull you coax with the string or cord. And remember, if you are making a 3/4" hole ( and that's what you should use), you pull the whole coax thru the hold from the outside, then terminate the antenna connector after you route the coax. You can put a 7/8" hole in, and then feed the mount from the inside, but you lose some ground connection that way.
I say "pop" a hole because I always use a greenlee hole punch, I don't drill the hole out, I just drill a small hole to use the punch.