Unfortunately the documentation was lil messy and I was not able to do it.
Here is simplest simplest example.
Use command line client of Code Collaborator and type this command
ccollab adddiffs new Folder1 Folder2
Instead of new, you can write the review number which you have created at your server.
ccollab adddiffs 12345 Folder1 Folder2
I had problem about this, so posting here. May be this will help you as well.
Good thing is smatbears people are on twitter and they helped me.. Thanks guys.