My site http;//www.dogbarkings.com is a subdomain hosted by bluehost of another site I have. However dogBarkings is the main one i am working with right now but I have an issue where it looks as if content from dogbarkings.com is duplicated from the main domain i have luckiestpets.com, I´m guessing I need to fix this in the robot.txt but should I edit the dogbarkings one or luckiest pets one and what do i need to enter.

by subdomain do you actually mean sub-folder

yes a subfolder of luckiestpets.com.

provided you never link to the subfolder it will never get found, but the luckiestspets would be the robots.txt to use.

The issue I have is that DogBarkings.com is in a subfolder of luckiestpets.com, but dogbarkings is the main site. It was just the way it worked when i purchased hosting and domains etc, wish it had been the other way, but nevertheless dogbarkings.com is its own domain, however we¡hen viewed from a directory perspective its a subdomain of luckiest pets and so pages from dogbarkings are duplicated in the parent folder luckiestpets, yet I have in no way linked to luckiestpets from dogbarkings.

It will have been created as an "addon domain" rather than being a separate entity.

SE bot's don't/can't parse physical directory trees. Provided you don't have any kind of scripting that will create a navigation structure from the physical folder structure, it should never be found.