my bitch has just been mated.i have found she has a cough if it is kennel cough what can be done without harming her pups.

Kennel Cough is not usually treated with any medication except some people give cough mixture. However if the KC turns in to a chest or throat infection antibiotic are sometimes proscribed, can only suggest that you tell the vet the bitch may be in whelp. Where did she get the infection, do you know, may be from the stud.

A few years ago our bitch caught kennel cough after being mated the vet quickly started a course of sinulux antibiotics as these are safe to use during pregnancy and we nipped it in the bud quite early, she went on to have a healthy litter of 6 pups

Same here - my bitch caught it from the stud dog's kennel I think (the owners had a boarding as well as breeding kennel).  A course of antibiotics and she went on to whelp a litter of 13.

Just a thought, I think I read somewhere that some cough mixtures can't be given to pregnant women.  If that's right, then perhaps they shouldn't be given to a pregnant bitch.  It will say on the bottle anyway.