I agree, the pup is confused.
PUps don't see things as we do - by using paper, and encouraging him to go on it, you are basically saying in his eyes "yes it's fine, go in the house".
If you shout you may scare him so that he learns to hide behind the sofa, or worse becomes too scared to poo/wee in your presence so may revert to messing n the house when you have gone!!!

I would go back to basics - take him out yourself every hour, maybe more if he needs it. After sleep, play, eating, last thing at night, and early morning. If possible, consider getting up at night to take him out as this will make things progress faster.
Use a word for weeing, i use "Quickie" and reward with a tasty treat - sausage, cheese, chicken etc. as this will again help him to learn more quickly that this is the good thing to do :)
Lindsay