Barking and peeing at the wrong place, help

[MyDuke]

I have an issue, Duke will be 2 in Oct and has been doing great with his pee pad and the barking, but for the past 2 weeks, Duke has been barking at nite while I'm sleeping. The worse part is that he gets to sleep with me in my bed, but he would go to the windows and bark at the noises outside.
It got so bad last nite that I think one of my neighbors ran my door bell (we live in an apt building).
I dont know what to do bc he gets all the exercise he needs when I walk him and play catch with him.
I tried the coins in the can, the spray bottle and everything, I have had to get out of bed, go pick him up and physically put him back to bed, but that would only last for a while. He typically stops around 3AM.

The other issues is I recently washed my couch cover and came home to find stain mark on the newly washed cover and that stink up my couch too.
He pees and poop on the pad, so is it that he's marking?

It's so frustrating sometimes with these little ones. I love him to death but days like this make it difficult; especially when he just turn and look at me as though he is the most innocent thing in the world.