There are a few things you could do besides putting your puppy outside by himself. Are you crate training him? Have you started training him to walk with a leash? How much time is he spending outside by himself? If he does'nt get along with the cat, the cat can easily get away from him, and you could put the cat in another room for a time as well. He's too yong to be happy sitting outside by himself, especially if you're home. Do you work outside of the home?
My puppies cry when they want more attention. Or when they don't feel good. Sometimes they just want to be held and they'll go to sleep. I think putting him out in the yard to "fin for himself" might not be the best of things. He could be going through a clingy stage, much like children do. Try some real one on one time with him, walking him on his leash for a little while, playing with him and maybe getting him interested in his toys to occupy him while you are working. Good luck!!! :)