Question

how do we calculate bond order of a molecule that has 3 different elements, like for example C-N-O

Answer 1

Here is a site that talks about bond orders and how they are sometimes averages and not always whole numbers.
http://en.wikipedia.org/wiki/Bond_order

Here is a site that gives a couple of resonance structures for the cyanate ion. You can figure the average from this.
http://tannerm.com/lewis.htm