I agree he is confused and I hope all of these suggestions don't confuse YOU. yikes.
I think you have to decide what works best for you and your pup and what your future goals are? (going outside only? inside on pee pads? or both)
No matter what you want you have to limit his free space.
In my opinion wee pad training is incredibly easy. Get the xpen..put a wee pad in one corner...bed in the other and toys and food/water in between. You will have to set this up in a noncarpeted area or protect the carpet with something. When you catch him going on the wee pad make a huge deal out of it and give him a tiny piece of treat. When you see him make a mistake...don't say a thing (for now) but clean up the smell in a hurry. Keep him confined until you see him being more successful than not. and when you do let him have more space....limit it and make sure his xpen bedroom is very available so he can run to his potty.
My pup learned on a wee pad...moving it to the outside was no big deal. It was easy b/c at first I just moved a wee pad outside. Now she will go on command
wherever but she is almost 5 months old.
at 12 weeks she spent most of her time in an xpen. Maybe other breeds can learn that young but many of us didn't even get our pups until they were 12 weeks old!
good luck and keep us posted. everyone here really does want to help...many of us have been where you are