the basic rule is that most tunnel sections should be -8 z's but it depends on the entrance piece, i know one is -12.
its abit of trial and error but it's pretty easy to figure out.
as Acid said, check the tuts ( mine also
) then at least u will have the blink groups sorted out then u will be able to see where the misplaced tunnel pieces are underground.
you may notice that some entrance pieces have a number next to them int he mission editor. that is the depth that the pieces attaced to it need to be.
and always use absolute height to get the pieces at the correct height